I just got my Alphatrack yesterday and the same thing happened to me. It worked fine when I installed it, but when I turned on my Edirol keyboard Logic complained that the 'Alphatrack' MIDI port was missing and the Alphatrack seemed to be frozen.
I tracked it down to what appears to be a Logic 9 bug. It seems that instead of using the interface name as configured in the Audio/MIDI tool it seems to be enumerating active interfaces at the time you configure a control surface. If you start a new MIDI interface that moves the Alphatrack position in the list, it will stop finding it and disable input for the Alphatrack as a control surface and will instead treat data from the unit as a regular MIDI stream.
I went to Preferences->Control Surfaces->Setup, selected the Alphatrack icon, and in the inspector on the top left reselected the 'Alphatrack' port for input. At that point, it started working normally again and the keyboard was not affected. I haven't turned the keyboard off since discovering this, but I suspect I'll have to perform this step every time the number of active MIDI interfaces changes between or during Logic sessions.
Again, the Alphatrack unit isn't sending anything different in it's data stream (verified by using a midi monitor program). I'm sure this is a Logic 9 bug. It also seems to be confined to Logic, as I installed the Garageband plug-in and it did not have this problem.