disappearing files and folders

Anyone else having this problem? On two separate computers now I have had to
try and fix corrupt jpg and mp3 files after windows update. Also there are
now many folders that have a size listed as 0 bytes but can't be deleted. I
have tried every fix I can find for this but no luck, only a format and
reinstall will get rid of those "dead" folders, but I would like to find the
cause of the data loss so I can stop it in the future. Also the fact that I
just spent many hours recovering lost family photos for clients, the files
are all there, windows just loses track of them and they can't be opened, but
the folders end up in a sort of "limbo", it shows as an icon but can't be
removed.
These machines are running Windows XP and unfortunatley had auto updates
turned on, so I am having a hard time figuring out which update is causing
the problem.
Thanks in advance for any help!