Figured out how to add to the exception list, only problem is that it doesn't disable scrolling, just the touch cube gesture! *smacks forehead". Anyways, I've added a guide below in case someone else needs this. Any more ideas anyone?
#1. Find the programs ClassName;
To do this you will need Fdc task manager, apparently the creators of this app know everything about PPCPE except how to make an icon that looks nice
Anyways, put a link to the task manager in your start menu and start up the app you want to add to the exceptions list.
Now minimise it, this may be a bit tricky. I managed it by pressing an app button (Messaging, PIE, camera etc.) and then the start menu button.
Start Fdc Task Manager and go to the process list, then hold the stylus on the program you want to exclude and click details. Now click Windows and look for the one you want (In most cases the second entry) the text in parenthesis ("") is the window title and the text directly after that is the ClassName needed.
#2. Add to the exceptions list
Now create a new key in HKLM\Software\HTC\Biotouch\Disable4SpecificApp
Lets say you called it "AGame"
So you now have the path: HKLM\Software\HTC\Biotouch\Disable4SpecificApp\AGame
Add a string value in this key called "ClassName" with the value of the ClassName found using the method above.
The cube will now not be activated by the down->up gesture whilst the window with that ClassName is focused.