After a long session of programming my new head unit, the convertible top had trouble closing, and the rear windows remain down. Could a weak battery cause this?

There are only Two things in the right rear the pump motor and the top ajar switch. This sounds like the motor is locked up or the top is jammed or going the wrong way. First disconnect the motor and if the noise stops it's the hydraulic unit trying to move the top watch the top to make sure it's going the right way, the top ajar switch could be bad. If you're confident in the hydraulic unit and motor the only thing left is a jammed top, a bad connection at the hydraulic unit, or the top ajar switch. I hope this helps. Take care.

Principles of Operation
Convertible top operation is controlled by the smart junction box (SJB). When the convertible top raise/lower switch is operated, the SJB commands the front and rear windows to the full down position. Window operation is disabled while the convertible top raise/lower switch is being operated. When the SJB receives a full down input for both rear windows, it commands the appropriate relay closed to raise or lower the convertible top. If the SJB does not receive a full down input signal for both rear windows, the convertible top operation is disabled.

The convertible top hydraulic system uses a 12 volt reversible pump and motor assembly. When active, the pump uses hydraulic pressure to extend the hydraulic lift cylinders to raise the convertible top, or retract the hydraulic lift cylinders to lower the convertible top. The convertible top motor/pump assembly is equipped with a thermal circuit breaker. The circuit breaker typically resets after 5 minutes depending on the ambient temperature. The thermal circuit breaker cannot be repaired and must be installed as a unit with the motor/pump assembly. In the event of a hydraulic system failure, the convertible top cannot be operated manually.

Inspection and Verification

1. Verify the customer concern.

1. Visually inspect for obvious signs of mechanical or electrical damage.

Visual Inspection Chart Mechanical Electrical

• Convertible top brackets and frame
• Convertible top latches
• Convertible top pump and motor assembly
• Hydraulic lift cylinders
• Hydraulic lines

• Bussed electrical center (BEC) fuse(s):
  • 13 (40A)
  • 51 (10A)
• Circuitry
• Convertible top pump and motor assembly
• Convertible top ajar switch
• Convertible top switch
• Connector(s)
• Convertible top raise relay
• Convertible top lower relay
• LH or RH rear power window motor
• Smart junction box (SJB)
• BEC

1. If an obvious cause for an observed or reported concern is found, correct the cause (if possible) before proceeding to the next step.

1. If the cause is not visually evident, connect the scan tool to the data link connector (DLC) and select the vehicle to be tested from the scan tool menu. If the scan tool does not communicate with the vehicle:
   • check that the program card is correctly installed.
   • check the connections to the vehicle.
   • check the ignition switch position.

1. If the scan tool still does not communicate with the vehicle, refer to the scan tool operating manual.

1. Carry out the scan tool data link test. If the scan tool responds with:
   • CAN or ISO circuit fault; all electronic control units no response/not equipped, refer to Section 418-00 .
   • No response/not equipped for SJB; refer to Section 419-10 .
   • System passed, retrieve and record the continuous diagnostic trouble codes (DTCs), erase the continuous DTCs, and carry out self-test diagnostics for the SJB.

1. If the DTCs retrieved are related to the concern, go to the Smart Junction Box (SJB) Diagnostic Trouble Code (DTC) Index.

1. If no DTCs related to the concern are retrieved, GO to Symptom Chart .
2. Smart Junction Box (SJB) Diagnostic Trouble Code (DTC) Index DTC Description Source Action B1141 Convertible Top Full Down Position Switch Circuit Failure SJB Go To Pinpoint Test E . B1142 Convertible Top Full Up Position Switch Circuit Failure SJB Go To Pinpoint Test E . B1402 Driver Power Window Down Switch Circuit Failure SJB Go To Pinpoint Test A . B2068 Convertible Top Up Output Circuit Failure SJB Go To Pinpoint Test A . B2069 Convertible Top Down Output Circuit Failure SJB Go To Pinpoint Test A . B2481 Convertible Top Up/Down Switch Fault SJB Go To Pinpoint Test A . B2578 Passenger Power Window Down Switch Circuit Failure SJB Go To Pinpoint Test A . All Other DTCs - SJB Refer to Section 419-10 .
3. Your best bet ,take it to a qualified repair shop !

NOTICE: Make sure no obstructions are present in the window system when carrying out this procedure.
NOTE: A battery disconnect does not require this procedure to be carried out unless the battery was disconnected while the window was operating.
NOTE: Excessive bounce-back (bounce-back that occurs with no obstructions present) may indicate a non-initialized window motor.
NOTE: Carry-out the de-initialization of the motor before initializing the motor.
NOTE: The motor will only operate in the 9-16 volt range. If the voltage drops below 9 volts, the window will not function correctly or may stop moving. If the voltage drops below 9 volts while the motor is operating, the motor will become de-initialized and will need to be initialized.
NOTE: The front window motors must be initialized whenever: a new window regulator and motor is installed, a new window glass is installed, a glass top run removal and installation or when carrying out any operation in which grease or lubricants are applied to the window system. A new front window motor is in a proportional up/down mode until initialized.
NOTE: The convertible rear window motors do NOT need to be initialized as they do not have one-touch up or one-touch down functions.
NOTE: All front window components (window glass, window regulator, window motor and glass top run) must be installed/tightened and adjusted to specification before carrying out this procedure.
NOTE: If this procedure is only partially completed, the front window motor remains non-initialized and only the proportional up/down functions operate. A non-initialized window motor may allow one-touch down operation, but does NOT allow one-touch up operation.

De-initialization then re-initialization

The motor can be de-initialized in 2 ways:

Disconnect the battery cable from the battery while the window is operating.

Remove the window motor fuse while the window is operating.

After the motor has been de-initialized, the initialization procedure must be carried out.

Make sure there are no obstructions present in the window system when carrying out this procedure. The door MUST be closed during this procedure (for convertibles, the top and quarter glass must be in the closed and up position), in order for the door window motor to initialize.

The windows must be in the full open position for this procedure to operate correctly.

Press and hold the window control switch in the UP position at the second detent until the window glass stalls into the glass top run for at least 2 seconds.

Once the top run is reached, hold the window control switch in the DOWN position at the second detent until the window glass stalls at the bottom of its travel for at least 2 seconds.

Cycle the window glass an additional 5 times to set the window soft stop for the down position.

Test for correct window operation by carrying one-touch up feature.

Good luck, if for any reason you can't give four thumbs up, please ask for more information. Thanks!

The rear windows are controlled by a timer in the top's ECU. If
the rear windows stop fully closing before your top is closed, the
problem MAY be with top's hydraulic system.

Check your top's hydraulic reserve tank for low fluid level. Lack
of fluid will greatly delay the top's closing sequence, leaving
those rear windows partially open.
Your top's hydraulic pump system is located beneath the right side
of the cubby/storage box behind the front seats. Raise the cover
and you'll see a removable trim panel on the right side. The pump
is behind that access panel.

You can use power steering fluid to top off the tank, but don't
fill it above level indicator line. You may have to add more fluid
after you cycle the top up and down to get the air bubbles out of
the lines.
It could also be a relay. On a 95 the relays that are in the trunk above the battery.
Perhaps, just switching the relays might prove which one is failing..

Hi I have the same problem on my 1999 Carrea, I had the windows at the rear stuck down and the roof latch keeps open and closing, I have not solved this yet it could be a relay but it all started when I was opening and closing on the keypad, if you get the roof up and cant get the rear windows to close get the roof closed to a locking position and where the hood lock pulls back at the roof lock station slide a thin s crew driver up the side of the lock hook they close then, also a tip, if you stick your little finger in the hole where the hood lock goes and press both the rear window buttons up they close when the roof is down. if anyone knows why my hood wont lock please let me know

Manual roof procedure
The procedure in the manual is just for closing the top.
A) Turn key to OFF for several seconds to bleed off hyd pressure.
B) Turn key to MAR (full electrical, but before start)
C) Remove cap on bulkhead behind the right-hand seat and use flat head screw driver to unfasten the hyd unit valve in order to relieve the oil pressure in the circuit.
D) Remove the cap on the bulkhead behind the left-hand seat and using screwdriver or allen wrench press until the top covering (panel behind roll bars that covers the convertible top well) until the panel's locks are released - you may have to tap the wrench to release the locks.
E) Lift the top covering manually and keep it open while extracting the top from its well.
F) Remove top from well until the front part is near the windshield frame.
G) Lift the rear part of top (rear window) upwards and lower the top covering until the hooks are resting on their respective locks.
H) While still keeping rear part of convertible top lifted upward press Button 1 to attach the top covering locks.
Button 1 is the forward one
Button 2 is the rear one.
I) Make sure locks are fastened. if not - try pushbutton 1 again. If necessary repeat D and H
J) Rest rear part of convertible top on top of covering.
K) At front of convertible top, open (deploy) the top's hooks by using allen wrench to turn the pin mechanism. (located in center of front headliner)
L) Press top unto windshield frame and use wrench to lock the hooks.
M) Press the rear of convertible top, so hooks on rear top insert into respective slots and press Button 2 to secure.
N) Keep Button 2 pressed until hooks properly fasten.

If the top is still tightly latched at the front, you can just start at step "G":
While holding the back of the top in the air, and the "top cover" resting down on its "hooks", press button 1 until it seats well.
Then lower the back of the top down to mate its "hooks" and press it down while holding button 2 until the top seats well.

do you see any visible reddish in color in the vehicle or on the floor ?

Window may not be initialized. Follow this proceedure

Window Motor Initialization Printable View (96 KB) NOTICE: Make sure no obstructions are present in the window system when carrying out this procedure.
NOTE: A battery disconnect does not require this procedure to be carried out unless the battery was disconnected while the window was operating.
NOTE: Excessive bounce-back (bounce-back that occurs with no obstructions present) may indicate a non-initialized window motor.
NOTE: Carry-out the de-initialization of the motor before initializing the motor.
NOTE: The motor will only operate in the 9-16 volt range. If the voltage drops below 9 volts, the window will not function correctly or may stop moving. If the voltage drops below 9 volts while the motor is operating, the motor will become de-initialized and will need to be initialized.
NOTE: The front window motors must be initialized whenever: a new window regulator and motor is installed, a new window glass is installed, a glass top run removal and installation or when carrying out any operation in which grease or lubricants are applied to the window system. A new front window motor is in a proportional up/down mode until initialized.
NOTE: The convertible rear window motors do NOT need to be initialized as they do not have one-touch up or one-touch down functions.
NOTE: All front window components (window glass, window regulator, window motor and glass top run) must be installed/tightened and adjusted to specification before carrying out this procedure.
NOTE: If this procedure is only partially completed, the front window motor remains non-initialized and only the proportional up/down functions operate. A non-initialized window motor may allow one-touch down operation, but does NOT allow one-touch up operation.
De-initialization

1. The motor can be de-initialized in 2 ways:
   • Disconnect the battery cable from the battery while the window is operating.
   • Remove the window motor fuse while the window is operating.

1. After the motor has been de-initialized, the initialization procedure must be carried out.

Initialization
NOTICE: Make sure there are no obstructions present in the window system when carrying out this procedure.
NOTE: The door MUST be closed during this procedure (for convertibles, the top and quarter glass must be in the closed and up position), in order for the door window motor to initialize.
NOTE: The windows must be in the full open position for this procedure to operate correctly.

1. Press and hold the window control switch in the UP position at the second detent until the window glass stalls into the glass top run for at least 2 seconds.

1. Once the top run is reached, hold the window control switch in the DOWN position at the second detent until the window glass stalls at the bottom of its travel for at least 2 seconds.

1. Cycle the window glass an additional 5 times to set the window soft stop for the down position.

1. Test for correct window operation by carrying one-touch up feature.

Try using the all windows up and down button (Drivers side on door), evidently after you change your battery this is the reset proceedure.