Incidentally, I've tried 3 different drivers on Mac OS: Built-in NTFS (read-only), NTFS-3g (via MacFUSE, read/write) and Paragon NTFS for Mac OS X (read/write).

Browsing through Finder actually shows a blank document icon for the folders it can't read. Browsing with PathFinder (my default) simply doesn't show the problem folders at all (which if why I didn't see them originally).