PokerTracker

Had trial version for a few days which was working fine. I registered today and now my stats are showing up on the wrong players and the mucked hands after showdown are going to the wrong players. I have my table set to 6-max and cant figure out why it suddenly stopped working correctly.

PT3-HUD or PAHud?
I guess you mean PT3..
What site?
Are you using some type of preferred seating?

Im using PAHud on stars and I wasnt using the preferred seating but I tried it to see if it would work and it had no change. Still showing up in the wrong spots whenever I switch seats at a table.

Moving seats after you sit down will not work because info about your new seat is not included in the hand history.
Preferred seating should work if you set the general option in stars before sitting and in PAH.