OK, just to make sure you're doing what I meant:
1. Go to "Import" tab - "Auto Import" tab
2. Make sure that under "PokerStars configuration", you have correct path to HH file. Thick on "Automatically start with auto import". Note that this only tell PT3 to automatically import Stars HH every time you do #3 (see below).
3. Every time you want to play, you must press "Begin Auto Import".
I believe your problem have no correlation with tabletracker but I might be wrong. I'm just an usual user.
If you need more help you can always sent them ticket on their website. They usually reply in 24 hours.
Good Luck