I've finally worked out why only some of my tunes got track numbers when uploading - the one thing that distinguishes the ones that do from the ones that don't is that the former have ID3v2 tags and the latter only ID3v1.

This is with the 2.0b7 emptool - the 2.0b11 release notes don't mention any emptool changes, so I assume this is still there.
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Toby Speight
030103016 (80GB Mk2a, blue)
030102806 (0GB Mk2a, blue)