OK, try this.
Turn preferred seating OFF in both pokerstars and PT3, then join a table.
The stats should be by the correct seats, and if you PT-icon -> Configure Stats it should say the correct table size in the title bar of the HUD config window.
If you don't see the correct table size, check that AQTL is enabled. If it is and you still see the wrong table size, Please
enable logging, reproduce the problem by playing a few hands on a single table and submit your PokerTracker.log and PokerTrackerHUD.log files (zip/compress them first, call it logs.zip) to the
Support system , and link to this thread in the reference field of the ticket so that we can investigate.
If you see the correct table size but the stats are in the wrong places, right click drag them to the correct places, then PT-icon -> Save Layout.
When you open a new table, the stats should now appear in the correct places.
Once you get to that state, enable preferred seating again in both Stars and PT3, and everything should line up.
If not, send us your log files as above.