Domi,
Try resetting the OnGame database and see if that helps: on PT3's auto import tab, click OnGame, then click OnGame Configuration at the right and "Clear Databases Now". This will not harm your PT3 data in any way.
If that doesn't help, please enable logging (Configure --> Options --> Logging Enabled and restart PT3) and import while playing for one full orbit on a single table and then attach the C:\Program Files\PokerTracker 3\PokerTracker.log and C:\Program Files\PokerTracker 3\PokerTrackerHud.log files to a
support ticket and we'll look into what could be causing this for you.