Hi, when I replaced my Digidoor 3 main board, I followed the manual instructions to reset the limits but the door goes down once and then instead of returning automatically and then beeping twice to show the limits are set, it beeps twice after one direction and when I try to use the remote it shows communication but the door does not move?

It is always better to get the remote for the door make you have. The same seller does a 4 button remote as well.

Digi 2 button remote transmitter for Digidoor motors (replaced ...

www.mrremote.co.za > product > digi-2-button-remote...

Sold with DigiDoor II (2), DigiDoor III (3), DigiDoor IQ and DigiDoor one garage door motors. This remote is also referred to as a Digi"e"Key, Digi Ekey, Digikey, ...

There is help here.

https://www.google.com/search?q=program+my+nova+remote+for+my+digidoor+2+garage+door

..

this is your manual https://www.manualslib.com/manual/1077322/Hydro-Doors-Digidor-Iii.html

Hi there Vusi.
You should have a manual open and close switch on the wall for your Digidoor. You need to find the two wires which control the open and close functions on the Digidoor Trace these back to the Digidoor motor connect these to the Comm and NO terminals. You also need to supply 12V power to the receiver This needs to be connected to the Possitive and Negative terminals on the receiver. These connections originate in the Digidoor motor housing and can be connected right there. Some Digidoor motors have connection terminals for additional remote receivers in the housing. Remember that the minimum connections needed are Positive, Common(Sometimes the common is also the negative supply so you can bridge the common and negative terminals on the receiver) and NO. Then pair the remote with the receiver as per the instructions in the receiver box. If you still cannot come right post pics of the PC boards of your receiver and Digidoor motor and I will identify the connections for you

Limits must be programed. Power down and remove battery power ,press & hold button on motor pc board then apply power still holding button. The door should start running open and close. When it starts you can release button

"Another reason is problems with the radio frequency of the remote control system used, some older systems use frequencies that are liable to interference from various sources such as police and fire department radios and military communications. The effects of this interference are many for example, the garage door may open and close on its own or the operating range of your remote control may become so poor you cannot open or close the door with your remote control even whilst standing next to it."
source

Thank you for including timer model number.
You have almond-colored ST01AC timer that worked before and then stopped working.

The manual override no longer turns lights on-and-off.
Manual override works by pushing in timer door, and also by pushing on-off button on face of timer.
1) Try pushing on-off button directly instead of timer door, in case little plastic point on timer door has worn down. If timer door is worn down, maybe add a few layers of tape so door can push button again.

2) If timer on-off button is not working, then timer may be defective -or- timer CR2 battery needs to be replaced, and then timer reset and reprogrammed.

3) Defective timer: timer has 1 year limited warranty against workmanship defect
http://www.intermatic.com/customer%20service.aspx

4) Replace CR2 battery, reset timer, and reprogram timer and see if functionality is restored.
If timer is not restored, then timer is going bad.
Open following link for illustration of battery replacement, steps for resetting timer, and illustrated re-programming steps.
http://waterheatertimer.org/ST01C-program.html#battery

5) Take a moment and rate answer:
And take advantage of fixya expert assistance live.
For a price, expert works with you while you work on timer or any do-it-yourself project.
Fixya is always less expensive than a service call.

You are receiving interference from the digi door. You will have to return this unit and go with a different one on a different frequency. Chamberlain makes a clicker that would work well with that unit. Thanks BB

BE SURE YOU HAVE THE CHAIN/BELT INSTALLED PROPERLY.
IF THE DRIVE IS AT OR NEAR THE UP LIMIT SWITCH THE DOOR CAN'T GO UP.
LOOSEN & REMOVE THE CHAIN/BELT.
TRY RUNNING THE OPENER TO BOTH LIMITS - JUST TO SEE IF IT WORKS.
RUN THE OPENER TO THE DOWN LIMIT.
MOVE THE TROLLEY TO THE CLOSED POSITION - RECONNECT CHAIN/BELT.
HOPE THIS HELPS

Instruction book says to press the UP, DOWN and I buttons on the circuit board all together for 3 seconds. Then press the I button until the item you want is displayed i.e. the upper limit set point. Then press the DOWN button until you have set the temperature you want. After 60 seconds without any inputs, the temp is set and the system goes back to READ mode.

I just got one and need to set my upper limit from 130 to 140 degrees. Showers are a bit cool.

Hope this helps.