Are you using the miniview tables at Boss? At those tables you are always shown in the bottom centre seat.
PT4 should be able to detect when you are using miniview tables, but you need to restart both the Boss Client and PT3 for that setting to be picked up.
If that doesn't help it could be that PT4 can't find the settings file for your Boss skin. Please restart PT4 and play a few hands at a single table and attach the PokerTracker4.log file from C:\Users\yourname\AppData\Local\PokerTracker 4\ (which you can access from the PT4 File menu) to a
Support Ticket along with the hand history file for the session (you'll need to
compress that in order to attach it) and a
screenshot of the table window so that we can investigate further.