sarahkitten,
When you do this again, can you check that the uninstall doesn't leave anything behind in the Program Files/iTunes or Program Files/Common Files/Apple folders? Make sure that the Apple Mobile Device and iPod Services are not running. (Your library and media files should be kept in your music folder and should not be affected by this.)
Check to see what other programs you're running during the install -- Outlook, IE, FireFox.
Something is making the iTunes installer cranky so that it's not laying down all the new files / deleting all the old ones and I'm trying to figure out what it is.
Thanks