In the last 4 days, I have booted it up only to have between 8000 and 9500 updates on three occasions. Yesterday it booted up to install 13 updates, then after that it went straight to 8000+ updates. This update screen is not the blue windows screen with the blue circular icon (mouse pointer), but it is a black screen with grey letters. I watch and the majority of the updates are going to /Registry/machine & /Registry/machine/Schema ..... .
If the computer is way behind on updates, there might be a backlist of dozens. Since some of them often must be loaded in a specific order, some will fail the update and reappear the next time, so it can take a number of runs to work your way through the list. I'm not aware of anything from Microsoft that just updates registry entries, and even if there was, it would never be in the quantities you describe. I don't know exactly how many entries there are in a typical registry, but I'm guessing that you could recreate the entire thing with the cumulative quantities you describe.
Updates replace programs. The registry doesn't contain any programs, it is basically just a big, centralized list of settings. There is no legitimate reason to change or add massive numbers of entries. Also, the black screen you describe sounds like something is being run in a command window. A lot of maintenance gets performed in Linux in a command window but not typically in Windows.
Whatever is doing this doesn't belong there. It is behaving like malicious software, although it's possible that some program got seriously corrupted. If the AV programs don't find anything, you should use a more serious approach to stop it or you are likely to find that the computer will stop working.
Try booting in safe mode with command prompt. Then run msconfig and see if anything unusual is listed. You also have nothing to lose running SFC /scannow. It doesn't sound like something this will fix, but it can't hurt to try.
If the problem is being caused by something that is part of the Windows distribution package, there is a way to replace Windows "in-place" without losing everything else. You need the Windows installation disk to do it. Not very many computers come with them any more; you get them when you buy the retail package, the OEM version typically just gets backed up to a restore partition. If you have the Windows disk, see this link:
http://support.microsoft.com/kb/2255099 It doesn't sound like the problem is caused by something that is part of Windows, but this is the next-least-destructive thing to try.
If that is not an option or doesn't work, the best thing to do may be to start over. I can't think of a clean, non-destructive way to get rid of a program that is not part of Windows if you don't know what it is and AV software doesn't recognize it. Use Safe Mode with Command Prompt to copy all of the user files to another drive or storage medium. Limit it to just your own (or her own) files; you don't want to save a misbehaving program, go through all the work of redoing the computer, restore your files, and have the problem start all over again.
Then recover Windows (reinstall it if you have a disk but not a recovery partition; if you have both options, do a recovery). Afterwards, it will be like a new computer. You will probably have to reinstall all of your software and configure everything like your email accounts, preferences for everything, etc.
