I had the same problem of the disappearing files. I then tried to process them again only to be told that it was already there. But a search could not find it.
It took about an hour but here is the fix.
You can either go to advanced search and tell it to look in unindexed and hidden files. That usually works. Another choice is to rebuild the index.
After that I just searched "EVERYWHERE" for *.mp4 and presto there were the files.
Apparently one of the quirks of Windows Vista is that it does not display files that are NOT part of the Index. Why this is I do not know.
I am also having a problem registering CloneDVDmobile on Vista. I managed it once. Then had to reformat the hard drive. Never been able to do it again. Any ideas???