This may or may not be what's causing your problems. Android has a media deamon that checks all the media on the devise when it is unplugged from usb communications. If it finds anything wrong with a file it deletes it with no warning.
The app "just playlists" helps because it at least gives you a clue as to what is wrong. It may be worth a try!
To be clear, the android media scanner scans the files and deletes any items in those files that it finds a problem with. So you would for example, end up with an empty playlist file if the directory paths in the playlist file were incorrect. You can prevent this by putting an empty file called ".nomedia" in the directory. If there is a problem with the paths in the playlist file you will not be able to play them but they will not be emptied. "just playlists" will put an empty ".nomedia" file in the directory for you and can help with playlist path problems.
Now this may or may not be the problem with the ring tones but it is worth investigating.
I had a major issue trying to transfer playlists to my S3 and the playlists suddenly disappearing. "just playlists" helped me find an error in the paths to the mp3 files.