E-46 resets all systems every time shut off - 2002 BMW 3 Series

When you disconnect the battery, you need to reset the security system and immobilizer.

https://www.google.com/search?q=1999+ford+escort+reset+security+system

The Fuel Shut off has a red reset button on it.

https://www.google.com/search?q=1999+ford+escort+reset+emergency+fuel+shut+off+system

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The 12 is normal for the starting code. The 41 says generator (alternator) field is not switching properly. Code 45 says Turbo boost limit exceeded (engine was shut down by logic module). I doubt that you have turbo on the Dakota. However there IS a code 46. Battery voltage too high during charging or charging system voltage too low. That would make sense with the 41 code. Sounds like you may have an alternator/charging system problem.

this system has a shut down mode when it detects freon gas is low. if the system is cooling the car just by being reset then you may have a faulty high or low pressure switch, but if it is reset and turned on and is not cooling the car correctly then that is why is keeps going into shut down mode. this was set up to avoid a/c compressor damage, this wont allow the compressor to run and over hat itself due to low or overcharge in the system.
the first step would be to evacuate the system and apply a vacuum for 45min. then recharge the system added oil and dye, (dye is used to find leaks if system looses freon.) then run a/c and do a vent temp. test, making sure compressor pressures are good and vent temp is good, at this time shut down car and see if it goes into shut down mode. if it does then have the switches tested and check the compressor clutch, ohm it. start with this, if the system takes a few days to go into safe mode then i would say there is a leak and it is doing its job, now you will need the glasses and blue light to locate your leak.

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Try doing a Passkey security system reset (procedure below), if that is not successful then you will need the dealer to scan the VATS module with controls the security system.

PASSKEY LOCKOUT RESET ALL GM CARS 1999 AND UP

1) Put the key in the ignition and turn to the "ON" position. Leave it that way for 10 minutes. After 10 minutes turn the key and take it out. Repeat this process (2) more times (3 times, 30 minutes total) This should reset the PASSKEY system to recognize your key.

if it is a factory system the following should reset it.

• Turn the ignition switch
  off.
  
  

• Insert the key into the driver's side
  door.
  

• Turn the key clockwise to lock
  it.
  
  

• Turn the key counterclockwise to unlock it.
  The alarm system recognizes an authorized key was used and the system
  resets.

you may have to do this each time you unlock the car.

if it is an aftermarket system you will either have to identify the system and serial number and try to contact the manufacturer for a replacement fob, or have the system removed completely.

46--- Driver Pretensioner Circuit Resistance High

That means the buckle in you driver side seat belt system has failed. It has an explosive device called a pretensioner in it which is designed to pull you into place microseconds before the airbag deploys. That component has failed and has deactivated the airbag system. You will need to replace the 'buckle pretensioner'.
But before you do, please get real familiar with the system you are working on before you cause additional damage, hurt yourself or deploy the bags accidentally.

http://www.airbagsolutions.com
http://www.airbagsolutions.com/vehicles_list.aspx
http://www.airbagsolutions.com/demo.aspx

Sounds like the system needs charged. When the pressure drops the switch will shut off the system. Hope this helps and have a good day.

Your car is equipped with a system called PASSKEY standard on all GM cars and light trucks, try the following procedure to reset the system, the battery being dead will trigger the system.

PASSKEY LOCKOUT RESET GM CARS 1999 UP
1) Put the key in the ignition and turn to the "ON" position. Leave it that way for 10 minutes. After 10 minutes turn the key and take it out. Repeat this process (2) more times (3 times, 30 minutes total) This should reset the passlock system to recognize your key.

Code 46 is indeed the trouble code for the Idle Speed Controller which is that big black box thingy on your throttle body. A lot of Chilton-type manual books omit that code because the ISC isn't found on pre 94 Metros. The ISC is a computer controlled auto-adjuster for the engine idle.

An important note: code 46 is often caused by misadjusted distributor timing. As you probably know, timing affects the idle, and if improper timing moves the idle beyond the ISC's adjustment range, the check engine light will come on and diagnostics will return code 46.