I had the same problem with FOMM. I managed to fix it by deleting all of the files in the Windows temporary files directory. Possibly FOMM unzips the fomod directory there and was choking when the intended destination already existed? Anyway, the directory is at (in Windows 8, at least) c:\Users\your_user_name\AppData\Local\Temp The stuff in there might be in use by running programs, so to be safe you might want to do a clean reboot (or even be in Safe Mode), delete the files, then reboot again. I haven't had any trouble after deleting these files, though (and it cleaned up several gigs of space!).
