Well, it doesn't seem to matter if advanced cleaning options are used or not. Default settings give the exact same result...
Since I'm unable to get Virtal PC installed at all, after another reinstall I've been trying to figure this out the hard way be by backing up (w/Reg Entries at least -- CCleaner really needs an option to move files to recycle bin when cleaned) and cleaning a few things at a time and rebooting.
I don't think file cleaning does it, unless it's related to an obscure log file (seems unlikely) or some IE index.dat files, and registry keys make the most sense anyways...
I removed all of the Unused File Extension and Invalid default icons entries, and this seemed to do nothing.
I removed all the Open with Application orphan entries pertaining to, in 3 separate groups, Windows Backup, DVD Maker, and Bitlocker, and none of these seemed to break anything.
And I removed all of the Missing Shared DLL entries pertaining to NET Framework, and after this everything seemed to break again. For some reason I also seem unable to restore these entries to the registry (I merge the REG file, but they don't show up in CCleaner again, unlike all the other backups) so this seems like a possible culprit... but who knows.
I suppose for the time being I'll just have to not use CCleaner... but with all the application and driver installations that are being a PITA and requiring multiple install attempts with various compatibility settings to get them (mostly) working I'm making an awful mess on my hard drive... heh.
The funny thing is, I had more Windows bugs, and less application/driver bugs when Win7 was still beta, but the RC build has reversed all that - The OS itself seems rock solid and ready to go RTM (less buggy than Vista even,) but all the app and hardware issues remind me of the early days of Vista when everyone was dragging ass getting their updated software out.
Who knows if we'll get a RC2 with MS wanting to get 7 out before the fall school shopping season starts, but hopefully a lot of software is updated in the next couple of months. Cross fingers, eh?