I haven't experienced the issue. But could the "some files not recognized unless converted again" issue be due simply to the Mac files or creator type or other misc Finder data attached to each audio file?
on the iPhone end, it is probably only recognizing audio files with certain file attributes and has very little to do with the audio encoding of the file itself?
I just tried what i thought might be the issue and it turns out its not. I removed all finder data etc from the audio file and it still didn't sync.
Removing the ringtone and putting it back did not work
Converting the ringtone from AAC to MP3 or vice versus did not work
What did work was simply quitting iTunes and iToner and relaunching. So I'm thinking it might have something to do with data or directory that iTunes writes to disk at intervals or upon quitting or launch?