PokerTracker

To clarify, I saved the layout I wanted when I was sitting in the top right spot on a table and uses it as default since. Another problem I encounter is that I no longer have the "treat as 6 max" button in the PT button in the HUD. Checking the "adjust qualifying limits" button doesnt seem to help.

Before I installed the beta, I was on another Ipoker skin and the HUD worked fine; now it doesn't work on any skin.

Please take a look at the Tutorial: Preferred Seating - the troubleshooting section there should help you get your layout issues resolved.

When AQTL is checked you shouldn't need to use the "treat as" option - are you still getting mislabeled sessions then?

The beta should work on all sites the stable version does - please report this problem so that we can investigate further for you.