Could be the WinSXS folder, which can be HUGE and is based on hardlinks which are easily upset by a change in port ID.
Being hardlinks, the chances are good that the "missing" space was never really missing, just a reporting error. (Not that it's excusable. Microsoft has yet to even acknowledge it as an issue....)
Ahh, I hadn't thought of that. I suppose that could be it.
Do you have any prior experience with port changes causing problems with hard links? I don't know much about how hard links are implemented internally by NTFS, but in *NIX file systems (e.g. ext4) the port ID is irrelevant when creating hard links.