I have discovered a bug in gtkpod. I have lots of compilations (both in MP3 and AAC format). For compilations ("Various Artists") I always set a flag in the ID3 tag of the files so the songs can be recognized as part of a compilation .
For some reason gtkpod does not classify M4A files with that flag as part of a Compilation (it is working for MP3 files). I've double-checked the tags with AtomicParsley and I am 100% sure that the flag is set to "true" on all of my compilations.
I guess this is an easy fix, as it is working fine for MP3 files with the same flag.
PS: For some reason I cannot open a new ticket in the project's bugtracker. If this is the wrong place for reporting bugs, please point me into the right direction.