1998 Chevy Cavalier Jerky gear shifts

The car is the Z24 version of the Cavalier. The transmission shifts are not always very smooth. One shift occurs around 2400 revs with a slight drop in revs then with the gear shift completing with a jerk. Accelerating harder from standstill makes the shift occur with a jerk at about 4000 revs. The shop I normally take it to advised me they had to reset the computers (2 of) as they were not talking to each other and the car had consequently gone into a 'limping' (default) mode. The car seemed to shift smoothly after this correction for a few drives but now seems to have reverted back to the jerky shifting. I will make a donation to help.