Hi, it's been happening to me also with Logic 8. I wrote a post about this, but found a solution, not the perfect solution, but one that, for the moment, keeps the Alphatrack working fine. You cannot switch off any controller. Keep them connected and ready every time you switch on your computer. Open a project. Then, if you get the message that the alphatrack is assigned to a MIDI port that is missing, go to control surfaces and delete the aplhatrack. Restart logic and open the same project. You'll see that Logic recognizes the new controller. From now on, it'll work fine unless you disconnect one of your controllers, or include a new one. In that case, you'll have to follow the same procedure again. And you have to to this with every project.
Anyway, this isn't a convenient solution, so I'm waiting for someone to solve it, but, if you read the post about the compatibility with 64 bit Logic, you'll feel, at least, alone. And I think that bought the Alphatrack because I liked the Customer service...
Oh, by the way. The same problem happens with the Presonus Faderport