What are you using to keep your system "clean"? some clean up utilities are very aggressive, I've had occasions where the installer folder was empty!! In this case the Add and Remove Programs function stops working as it's searching for the installers!
I wouldn't think for a minute they've been "misplaced" in the wrong folders.
Also, to make life easier for yourself, in your folder view (View, Choose Details...), tick the "author" option to show who the folders belong to/what put them there.