Perhaps your library settings aren't generating properly? Others have suggested resetting to defaults through the Windows GUI, but it could be that something is preventing that step from completing successfully.
Trying resetting to default again, and then check the Event Manager snap-in. Look under System or Applications and see if any errors that may be related are shown.
If that doesn't shed any light, try going to this path in Explorer:
Your libraries will be listed in this folder. Double-clicking on them should open the library. If you right-click, though, you can open the file in a text editor (I was able to open them in Notepad++ using the Edit with Notepad++... context menu entry it can install with), and you'll notice that they're simply XML files. You should, at the least, be able to check that the XML syntax is correct by eyeballing it. They should look similar to the example shown here: http://msdn.microsoft.com/en-us/library/windows/desktop/dd798389(v=vs.85).aspx#libraryms_example
If Windows is generating corrupted XML files (assuming your attempts to reset to default as others have suggested didn't fix it), I would suppose that you have bad sectors on your hard drive and those files are getting partially (or wholly) stored on them. Try running scandisk and seeing if it detects anything. If it does, it should mark those sectors as bad, and cause Windows to try and recover those files elsewhere, or at least the next time you regenerate them they'll be stored elsewhere on the disk.