Are your tables overlapping? There have been issues with overlapping OnGame tables causing HUD problems.
If the tables aren't overlapping, please enable logging (Configure --> Options --> Logging Enabled should be checked, then restart PT3) and play for an orbit on a single table trying to move the stat boxes several times 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 it further.