Please read the FAQ: PT3 HUD for tuning tips. In particular, if you get a lot of duplicates reported when you start Auto Import please read the Tutorial: Preventing Duplicates.
Enable logging and restart PT3. Start Auto Import and then play at a single table. Note the time that the HUD appears and attach the PokerTracker.log and PokerTrackerHUD.log files to a Support ticket along with the hand history file for the table.