Thanks!
I'm having the same behavior.
When saving from Inkscape, everything looks fine, no error message, but then, when going to the actual location in Programs files through Windows Explorer, the file is not there.
(Although if reopening Inkscape save dialog, the file is visible!)
I think this is folder virtualization feature in the works as I suspected above. In Vista and 7, programs runs with normal user privileges (even on an administrator account) so when Inkscape tries to writes to Program files directory, it is transparently redirected to another, safe location.
The files are virtualized into %localappdata%/VirtualStore