PokerTracker

1)Preferred seat doesn't work properly when choosing 'autocenter' or any preferred sit in the pokerstars client, the Hud for each player is misplaced.

2) Although I have chosen 'for everyone but Hero', Hud still shows all my stats from all the hands in the database.

Mac Os x 10.6.8
PT3 3.14.7

1) PT3 does not support the "auto center" option (PT4 does) so you will need to preferred seats for each table size you play. Make sure that your settings match between PokerStars and PT3. Please review the Preferred Seating guide for more information.
Please note that if you have the Memory Grabber option enabled then while you're waiting to post the blinds PT3 doesn't know you are at the table so will not rotate the stats. Do NOT reposition the stats until after your first PLAYED hand has been imported or they will be rotated to the wrong places again at that time.

2) Make sure you select the correct Hud profile (that you're using at your tables) before making the change, and that you OK or Apply the change.
Again, for PokerStars observed hands PT3 doesn't know that you are the hero so you may see your lifetime stats until after your first played hand has been imported.

I have already try all the options you mention. Hero Hud (without grabber) shows all the hands and not session stats. I did also turn off auto center on stars and did set different tables to 3 and also done this by PT3 than I did change all the tables to preferred seat 4 and also done the same in PT3, non works.

As I only play 6 max, it is easy to see that it doesn't work.

If I had to guess, I would say the seat issue comes from not recognizing me as Hero.

Please open a Support Ticket and report your problem so that we can check your logs and see what is going on. Please attach a screenshot and the hand history file from the table along with your log files.