Hello damionhill,
Sorry to hear you are among those having this problem. I understand your frustration.
But I think the point we are trying to make here is that it doesn't appear to be a problem specifically with the AlphaTrack's drivers. In fact, if you are seeing it with your AT then you will likely have the same problem with the Presonus or any other midi controller. Even one made by Digidesign themselves. For some reason, and only on certain machines, PT just isn't outputting the MIDI messages that it should.
On my office machines for example, I have no problems with PT8 and AlphaTrack. But we don't know why some folks do.
Some on the DUC forum have suggested that they fixed their setup by re-installing, or repairing PT8 AFTER installing the control surface drivers. As if maybe PT8 only sees drivers that are already in place when installed. But this looks like it didn't help in every case.
Other have tried deleting all of their Pro Tools Permissions folders. So far we don't know precisely what will work for everyone.
I just want you to be aware of the situation so that you don't get further frustrated if other gear doesn't work too.
CS