That certainly shouldn't happen; it should keep importing hands as you keep playing.
Please enable logging (Configure --> Options --> Logging Enabled should be checked, then restart PT3) and play for a single orbit while auto importing then attach the C:\Program Files\PokerTracker 3\PokerTracker.log and C:\Program Files\PokerTracker 3\PokerTrackerHud.log to a
support ticket and we'll look into what's causing this for you.