See this thread:
http://forums.winamp.com/showthread.php?p=2788699
Basically, it would appear that Winamp/the Default Music Player on Android do not read .m4a meta-tags (ID3?) correctly causing (at the very least) the track order to default to alphabetical. Then, since the MPEG-4 transcoder creates .m4a's when I transfer a FLAC-encoded album to my Android and it is transcoded on-the-fly it loses the track order data. I'll bet it loses all the meta-data but since the files are saved in the directory structure with Artist/Album-name they're at least still split by that data in the Winamp/Music player listings.
I'm running Winamp v5.621 and my Android phone is a Motorola Atrix 4G on the Bell Canada network.
Send me the Winamp and Winamp Android code and I'll fix this bug for you! (: (That is, if it's not an inherent Android issue, which it may be...)