Ummm, wow. Why would you install it on the root folder?!?!?
Windows Installer keeps track of files that were deployed as part of the installation, but it can't keep track of items that are created *after* installation. That's why sometimes you'll see things like log files and the like left behind after an uninstall.
To force a "clean" uninstallation, it's not uncommon to issue a DeleteDir on [INSTALLDIR], which is the path that the game was installed to at setup time. This makes sure to clean up any log files or miscellaneous junk that the game creates post-install. In this case, [INSTALLDIR] == your root drive. Very, very very unwise.
I've used deletions of [INSTALLDIR] in the past in my own projects, and they would have tripped up the person's machine in the same manner. I've just never, ever heard of someone installing an app directly to root. A subfolder of root, sure, but *IN* the root folder?
Lesson learned, I would say. Make sure to install to at least a subfolder here on out, for any product.