If you have set them as you like and then loading another table means that they are not adjusting to the correct seats it could be because PT3 is not able to detect that FT is set to use auto-center. The way to fix this is to re-install FT - sometimes it seems that the registry entry PT3 looks up isn't there for some reason.
When you first started PT3 and the HUD first appears on a table, the stats should be in roughly the right areas, but if you have auto center on and PT3 is not detecting it properly then it won't be able to adjust correctly, so they could be in the wrong places.
If that sounds like what is wrong for you, please try re-installing Full Tilt (make sure it is in English too).
After installing, turn auto center off and set up your layout then save, close tables, turn on auto center again and start another table.
If you still can't get it to work, Please
enable logging, reproduce the problem and submit your PokerTracker.log to the
Support system , and link to this thread.