So, I asked this at the old forum…crickets. So, I actually delved into trying to fix it myself with ProcessMonitor…not gonna happen. When making changes to the MMC settings, which I should point out also incorrectly display as “MC settings”, Cubase is making registry requests to to the WOW32.dll. So, means it’s a no go for fixing it at my level of expertise. I’ll ask some of the compatibility programmers at work…I suppose I could install it on my XP box, ProcMonitor THAT to see where it’s writing…manually make those keys available in Win7, but…honestly, it’s not worth it. It does suck that this is the ONLY issue I’ve had with the app under the 64bit OS. As much as I’m sure they’d like me to buy an upgrade…just for this? I do MIDI sequencing/VI hosting with the box…not really in need of the new audio features of 5 you know? But, ultimately, I’m done. It’s not worth $200 for me to go further. I’ll just not sync it. I can pull a submix over to the midi box just as easily and work that way. Well, obviously not JUST as easily, or I wouldn’t have tried so hard to fix this. 
Here’s the old thread if anyone’s interested. Wanted to put this out there, since I did take it a bit further. If you don’t need the transport to control/send MMC, C4 (final release) seems to work fine in Win7x64. FWIW.