Revisions can be tricky.
My guess is that the transition you are changing the assigning the revision in isn't doing things in the right order. Our actions are as follows(order is critical):
Set Variable: %Next Revision%
We have found any other combination does not work. Do not mess with the rev counters.
To add to Corey's suggestion, make sure the %Next Revision% variable set action is on all transitions. Most likey you are mising this on the minor revision transition.