I don't think the problem would be with Desktop Manager; it's usually pretty solid. If anything, I'd be suspect of Exchange/Public Folders since your personal contacts are syncing correctly.
Do you have the option to remove the device from BES, wipe it, and reactivate? If so, you may want to give that a try. Other than that, you may need to call RIM for support; they're generally pretty good.
I'm surprised no one else has chimed in on this one. Someone must have seen this behavior before.