That shouldn't be happening.
Please enable logging (Configure --> Options --> Logging Enabled and restart PT3) and attempt to import while playing two tables for one full orbit 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.