This is the relevant section:
1. PT3 may not have recognized the size of the table correctly.
You can identify this problem by looking at your Texas Holdem -> Sessions tab (click 'Refresh') and seeing whether the session is correctly listed as "6-max" (or whatever).
If you play at short-handed tables this information is not included in the hand history files for all sites, so you should enable the 'Adjust Qualifying Tables Limits' option on the Auto Import tab. This will tell PT3 to try to work out what size table you are playing at based on the number of players involved, etc., and will therefore be able to use the layout for the correct table size.
2. If the stats still don't line up correctly, then you should disable preferred seating in both your poker client and PT3 and then play a session on a single table (or observe a table if your site supports observed hands) and position the stats to the correct places for all seats in their 'natural' positions.
When you have them where you want them, click PT-icon -> Save Layout and then open a new table to check that everything is in the correct places. (Note that this will not affect any other tables you currently have open, so try it with a new table.)
Once you have this working, re-enable preferred seating in both your poker site and PT3 and then everything should line up correctly once you start playing at new tables.
Basically what you need to do is make sure that if you turn preferred seating OFF in both PT3 and AP then the stats are in the correct places when you play a couple of new sessions.
Once you have that right you can re-enable preferred seating in both. Make sure you define it for the correct table size - don't mix up 9 and 10 seat layouts for instance.