So I got this response from PokerTracker support:
Please note that there is a difference between the beta software and the current live iPoker software. If you haven't tried uninstalling and re-downloading / installing the iPoker softare please try that.
With the new iPoker software there is still a discrepency between the information in the hand history and the table window, but in most cases that should be handled automatically (although if there are multiple tables of the same type open then the table select Hud will still be required).
If you're still having problems after reinstalling the iPoker software please attach a new set of log, hand history and screenshot so that we can investigate further.
At first I didn't understand it, but then I googled up iPoker and apparentely there is in fact a beta software with this new look, and this is where PokerTracker apparentely has problems attaching HUD to the right tables because of a "discrepency between the information in the hand history and the table window."http://www.ipokerbeta.com/wp-content/uploads/2015/06/lobby-william-hill-ipoker-beta.jpg?7f22a0
Now if you go to any of the iPoker sites, William Hill, Everest, Ladbrokes, Betfair, Bet365, etc. When you download their poker client software you will always get this new version. What is this "live version" Dave is talking about? Does he mean the old versions? This beta is the current live version every iPoker site offers. There are no other versions to download. How is it that PokerTracker hasn't yet adapted to the new iPoker software? If there is no fix for this, PokerTracker really should update their supported sites list, because stating there is full support is a bit misleading I think.
This issue still feels so unresolved.