Whenever the automatic window motors are replaced or disassembled, they must be put into learn mode to reset the jam protection. The window system 'knows' where the top of the glass should be based on a learned value. Anytime the glass is moved without the motors request (taking off the regulator), the learned value becomes invalid, and auto-up will think it is jamming and automatically lower itself.
Unfortunately this is going to require removing the unit again to repair.
To put the window back into learn mode, lower the window so that it is in a 'good' position for removing the regulator.
Remove the regulator and motor from the door.
Paintmark the scissor gear so it can be assembled in the same position before reinstallation.
Remove the motor from the regulator.
Reconnect the motor to the door wiring.
Run the window motor in the "UP" direction between 6 and 10 revolutions of the gear (this tells the system it is far beyond its mechanical limits, and puts itself back into jam-protection learn mode.
Once you have rotated the motor "UP" (it MUST be "UP" direction) more than 6 revolutions, but less than 10, reassemble the motor to the regulator, matching your previous paint marks up.
Reinstall the regulator to the door, and attach the glass. Be sure you do NOT push the down switch at any time.
Once reassembled, push the "UP" switch to bring the window to the fully closed position.
Then run the window through its motions fully down and again fully up a few times, then check the Auto operation.
Jam protection should function normally now.