I haven't done it yet...putting it off as long as possible. But some people have mentioned restarting both the iphone and the computer before trying to install ringtones again. Also, if you're using iFuntastic, make sure you have the most recent version. Good luck.
I actually had better luck. Originally with the command line version I had installed CTU24 ringtone, and then used iFuntastic and had some success, but sometimes certain m4a files would not play. After upgrading to 1.01, doing the restore and using iFuntastic I was able to install CTU plus another one that had shown up on iPhone, but never played any audio before.