Maybe it is buggy for tracks shorter than five seconds (the "Kirby Lose" jingle, e.g., doesn't play at all).
Anyway, this seems to concern the Mac version, only. AO Linux plays them correctly - only the song length info is missing, as well. And the problems with Vagrant Story and Shadow Hearts exist on Linux, too.
By the way: I found another bug. This time it's a single Scream Tracker 3 file that makes AO (Linux) crash. The interesting thing is that I couldn't find a second one, yet. Anyway, the song I'm talking about is Carrotus.s3m (can be found
here) from Jazz Jackrabbit 2.
EDIT: Found another one - Tubelec.s3m (same soundtrack) has some serious glitches (wrong pitch in the lead synth, strange noises...). And looking closer, it seems like every s3m song has these problems, some more, some less. Looks like the Scream Tracker 3 support is a little buggy.
By the way: Does AO support Impulse Tracker files? Because apparently the ones I tried don't work.