rejetto, Vista treats file handling very differently, from what I've observed. It seems to use the USN journal extensively. If the PC shuts down improperly, Vista will partially rollback the changes. While I don't fully understand this behavior, let me give an example.
Compression of a file with 7-Zip into multiple parts (.001, .002 etc.)
If you watch the process in XP, you observe that the files get created and the filesize raises as XP writes them to disk.
file.7z.001 50000KB
file.7z.002 50000KB
file.7z.003 34560KB <== 7-Zip working on this one, currently.
If the XP PC shuts down improperly during the task, you are left with the partial files.
Now the same on Vista (SP1, dunno if it matters)
The files get created as on XP, BUT THEY ARE COMPLETELY EMPTY UNTIL THE WHOLE 7-ZIP PROCESS FINISHES!
file.7z.001 0KB
file.7z.002 0KB
file.7z.003 0KB <== 7-Zip working on this one, currently.
If the Vista PC shuts down improperly during the task, the files vanish.
It could explain the VFS corruption dilemma, you could try closing and re-opening the VFS (and the HFS.ini, for that matter) after saving them. Another possibility would be to allow "hybrid-saving" to file AND registry, to have a fallback method should something get wrong (doesn't work for portable, obviously).