Win7 PVM recovered from TM backup is missing a lot

I recently tried to clean up my venerable old Windows 7 pvm but found that many of the uninstall files required were just not there or not functional any more. So I decided to create a nice fresh install of 7, and then added only 4 or 5 extra programs that I needed. Several weeks later, on booting that pvm up, I got the dreaded chkdsk message about "unable to repair filesystem due to recently installed software" or something like that. So I went to the Time Machine backup, pulled a copy of the pvm from a couple of months back, and tried it out. To my surprise, what came up looked like a fresh Windows 7 install - it was missing my background image, it had the "normal" taskbar instead of the "classic" bar I usually use, and most surprising, going to 'all programs', there were NO programs installed!

I tried several other copies of varying ages from the backup, and they all appeared the same, as if somehow what Time Machine was putting on the backup from the pvm seems to have little to do with the actual state of the pvm.

I'm doing more experiments to see if I can install programs to it, back it up, recover it, and have the programs still be there but I was wondering if anyone has seen this before?