The byte-sexing (I know, but that's what it's called) issue (i.e. little-endian) in this case has to do with the format of the sound file. I.e. the sound file itself is big- or little-endian, and it would seem the sound engine does not support the sound in question. I.e. the underlying hardware is irrelevant, the sound library just doesn't reorder the bytes (which is kinda silly, doing so is simple and well understood).
One thing would be to make sure you are using the latest SunJVM (1.6), but as you've already noted, missing sounds isn't the end of the world, sort of a benign Exception in this case. At any rate, this does seem to be a pretty common problem.
[EDIT: The install package looks to come with a redistributed Sun JRE 1.5, but it's probably not too hard to get it to use a different version - one of the great things about Linux+Java, that's easy to hack. 1.5 media support was pretty much half-baked... 1.6 is at least three-quarters-baked

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