Thanks for reporting the problem, dominion_player_1!
After studying the game number you provided, I have to agree with Mic Qsenoch, that everything seems to be in order. You played Rebuild multiple times, always named Province as the card to skip, and then upgraded some Estates to Duchies (turn 6, 16, 25) and some Duchies to Provinces (turn 10, 18, 23), which is consistent with the upgrade path you described in your post.
Gaining a Province when naming Province also seems to condradict both of your behaviours that you assumed were implemented.
If you did any undos after you did a Rebuild that you felt went wrong, then this isn't captured in the log, so I can't see them and evaluate them.
If you could say which playing (turn number) of Rebuild has the problems you describe, this would help.