What are the names of the folders? And do you have two separate "Program Files" folders? If not, you don't have two distinct installations, because Windows shoves some stuff in there and you will have virtually no way of determining which files and folders belong to which installation. Why not just backup data, reformat, reinstall at this stage? As GX1_Man often points out, that can be a good opportunity to clear out all kinds of crud, and make your system lean and mean again...