The only other thing I can think of is the AlphaTrack/Cubase plug-in. If it's older than version 1.0.3 then the sync project and mixer selection has no affect on the AlphaTrack.
Try going here:
http://frontierdesign.com/Products/AlphaTrack/Downloads
scroll down to the 'plug-ins' section and locate the proper plug-in for your computer and version of Cubase.
Since you can use a 32-Bit version of Cubase in a 64-Bit computer you'll want to make sure you have the correct plug-in. The plug-in is for your version of Cubase so if you're running the 64-Bit version of Cubase you should use the 64-Bit plug-in and vice versa.
This plug-in should replace any other AlphaTrack plug-ins in Cubase's 'components' folder located here: c:/ProgramFiles/Steinberg/Cubase/Components
Re-launch Cubase, make sure AlphaTrack is configured properly in the device manager and see if it behaves any differently.
CS