In case anyone is still reading this thread:

I have found a solution for 99% of my gapless playback needs

I am running Ubuntu 12.10 and Banshee 2.6.0

I can transfer music files to a Sansa Clip 8gb player from Banshee and gapless works in FLAC and (converted) Mp3. Much of my music is legacy m4a and Banshee converts it to MP3 before putting it on the clip. It is flawless, no pause, no pop, nothing.

Banshee plays gapless in FLAC without a problem. The only issue left Banshee playing M4a files, which have a 1/10 second pop between tracks.

Anyone with a clue on how to get Banshee to recognize gapless in M4a, please respond.