There's something I don't understand about CGFE. If I import a patch with it, the game install folder stays modified. But if I then want to go in and edit anything, I run CGFE and choose not to import a patch, the install folder loses the backup folders it made with the patch. Why?
Do you have "Load mod into Explorer" ticked ?
It will do exactly what you said it is doing so I'm guessing that is the problem.
Once you have edited a file or imported a patch and have clicked "Create Mod" and close CGFE the next time you launch the tool you select the executable and then you select whatever you saved your mod as from the drop down menu.
Make sure when you run the tool you launch it with Administrator privileges.