In trouble and hoping someone can help

I haven't worked on my site for ages and have forgotten a lot of my previous CoffeCup skills, so maybe I'm doing something really silly. Anyway my problem is that I can work quite happily on files within the HTML editor, but when I try to find my files when outside the editor (ie where they're supposed to be in File Manager) they're not there. They don't seem to exist anywhere, even though inside the HTML editor they are displayed with the correct file path. They are being saved though, because when I open up the HTML editor again they are all there (thank heavens).
Recently, I was having problems transferring files (blocked because I didn't have administrator privileges) so I set myself up as an administrator and that's when my problems seem to have started. Having the Admin logon doesn't seem to have changed anything, so I'm not using it.
I'm using Windows 7 64-bit and have recently transferred my CC files over from my old laptop which used Windows XP. Everything seemed to be going fine until I added the Administrator user on the new laptop. I am using version 12, build 375 of the HTML editor.
Thanks for any advice.