jerky auto transmission

When I bought my car, they said the tranny had just been recently replaced. But ever since I'v had it, for a couple months now, the shifting has been pretty jerky. Could this be normal for a new tranny? Does it need time to be broken in or is there something wrong? Since our Jettas have a closed transmission system, I can't check the fluid level without taking it to a VW dealer. Or could there be a cable or something that can be adjusted to help the transmission shift smoother, like a throttle position cable or something. The reason I don't want to take it to the dealer is because the nearest dealer is 45 min. away and I work every day from 8 to 5. Any insight or suggestions would be great.
FYI, I have a 96 jetta Trek

Peace..