Well, I have the same setup as you (6800, Vista Business 32-bit) and don't seem to have this problem.
I have WMDC 6.1.6965 - the initial version didn't work. I setup the sync manager and so every time I plug in my phone I can go to Computer -> My Smartphone and browse \ and Storage Card directories.
Playing with the hidden folder options in Vista doesn't seem to do anything to the listing in my device, so maybe it's a setting on your device. I've probably done a lot of the random registry tweaks listed in the sticky, maybe something like the unlock hack has to be applied? Or some other setting you played with that I didn't?
Sorry if this isn't very useful, but not being able to replicate something makes it hard to solve.
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