Whenever you install AvP2 it should be to "C:/Program Files/Fox/Aliens versus Predator 2" or something similar. At least do this for Windows XP.
It seems that when you originally installed the game it went into the wrong folder, unless you're not using XP then its ok.
Use add/remove programs to uninstall the game first. Usually there are files that are left over from games that have to be uninstalled manually. These files are usually ones such as your player profile, settings, save data, screenshots, custom mods/maps/skins, etc.
So if any files are left over from installation, they aren't a big deal. You should be able to install over any leftover files such as the ones I previously mentioned (and install to the correct file path mentioned above as well). The game usually installs by itself, or you can run the installer off the cd manually. If it won't let you install at all, I suggest a system restore.
I can't think of anything else that may help you as what you listed is kind of vague.