No such issues for me, my m4a edited ringtones are all there in amongst the mp3's I have in a playlist titled "Ringtones". In iTunes the m4a's are listed under "Tones" and the mp3's are listed in a playlist called "Ringtones."
When I look at "Sounds" on my iPhone 5, all my personalised ringtones appear first, then the stock ones appear at the bottom of the list.