Why won't some music sync from iTunes to my iPhone 5?

Question

I have purchased several items from the iTunes store with no trouble syncing and playing on my iPhone 4. Recently I purchased two iPhone 5's for myself and my son. His phone is synced to my iTunes account and can play all content. My phone initially synced all my music and comedy albums. Occasionally I would come across a song my iPhone music player refused to play. I would touch the song name, briefly see the song/album and it would flip back to my playlist/song list without playing or it would skip to another song. Sometimes skipping several songs in between and flashing quickly the song title.
To rectify this, I researched the problem on the forums and tried one of the suggestions of right clicking on the song in iTunes, converting the song to AAC and then deleting the original and re-syncing. After powering down and re-syncing, the 173 non-synced songs out of 808 purchased songs were no longer even on my phone.
I accessed the iTunes store through the app on my phone, found the non-downloaded songs in the cloud and manually downloaded them to my phone. Although I couldn't put them in the playlists I had created on iTunes (where they are checked and the playlist is checked for syncing) I did have them on my phone and they played perfectly. After my phone was plugged into a power source with iTunes open and my phone synced, the songs were once again missing from my phone.
I contacted Apple support and we spent some time trying different things:
1) Selected tab under iTunes preferences for devices  "Prevent iPhone from syncing automatically"
2) Reset all settings
3) Backed up my iPhone for a restore - which we never did.
I spoke then with a senior support consultant and we then:
1) Deleted the songs from my phone through Settings > General > Usage > Storage where my playlists remained but were empty.
2) We re-synced all my checked playlists. The songs were still missing.
3) On iTunes we selected "Sync all music". Songs were still missing.
4) Went to iTunes Store via iTunes on my Mac, looked up purchases and downloads, re-downloaded missing songs (there were only six of them and happened to be the ones that I converted to AAC).
5) Created new "Test" playlist and dragged two of the missing iPhone songs into it. Synced phone to include new playlist. Playlist appeared but was empty.
I had purchased two John Pinette comedy albums. One entire album will not sync and on the second, only two of the thirteen "songs" will sync. The support person asked if I wanted to change all of the m4a songs to mp3 and was going to show me how but when viewing the John Pinette "Still Hungry" album where the first and last song synced, they show the file ends with m4a, as do all of the songs that won't sync. This leads me to conclude that the file type isn't the issue, but that there is something corrupted with certain files from the iTunes store or a glitch that is incompatible with the IOS 6.1.
Has anyone else had a similar problem and have you been able to rectify it?

Answer 1

I have a similar problem and have spent three sequential days at the Apple Genius Bar before we were able to exclude most other possibilities and found that certain files (in my case all mp3s from CDs I own) that play just fine in iTunes 11.0.1 and that used to play in iOS 6.0.1 do not play in iOS 6.1. We restored the phone to factory settings and synced only a few of the music files that were problematic. They still did not play. We reproduced the problem on my iPad mini (iOS6.1).
Apple Telephone Support suggestion was to convert all mp3 files in iTunes to AAC (which according to Apple Website may degrade sound quality). No further suggestions or escalation but a recommendation to place comments on www.apple.com/feedback and, if there are enough complaints, someone at Apple might take an interest in this problem. Something has changed in iOS 6.1 where files that played on prior mobile system software no longer work.
Apple, please pay attention to this glitch with iOS 6.1.