After saving a setup as a .factory file the name of the saved file should be visible somewhere on the screen- like in the title bar. As it is, it's too easy not to remember which file was originally loaded and hit ctrl-s, only to overwrite the wrong file.
Also, when using ctrl-s, there should be some visual indication that something has happened. Best would be to combine it with text in the title that would read something like "foo.factory- unsaved" beforehand, and have that change to "foo.factory- saved" afterwards, until the user makes any sort of change, at which point it reads "foo.factory- unsaved" again.