My 1996 Audi A6 was left over the weekend at the airport with the lights on, and after it was jumped, it wasn't acting normal. Shifting into 3rd and 4th gears, the car tends to go into neutral for a split second (which makes the engine rev if I don't immediately let off the gas pedal), then it jerks into gear. 5th gear doesn't seem to be acting normally, either, though it doesn't have the same issue.

Any suggestions?

 

Low battery voltage probably caused the adaptations to be garbled in the EEPROM of the TCM and ECM, not the jump start. It probably all happened when you turned the key to start it with the dead battery. Get it towed to the dealer and get it checked.

I doubt the ignition was on when the jump battery was connected, this is when the surge hits. You probably don't want the key on when connecting the jump.