Sitting fo a couple weeks

This has happened two separate times. When my car sits for long periods of time, for the first couple 1st gear engagemets, at the end of the shift I hear a clunk for lack of better a term. The acceleration feels kind of bumpy too. After a couple times it never comes back.

POWERSTROKE
When my 01 jetta started doing that it was low on tranny fluid and the syncros would stick for lack of fluid once you are moving the fluid covers everything no more sticking.
Evan