I do exactly as TedP describes to workaround the lack of track number sorting with soups in jEmplode. As mschrag indicates jEmplode doesn't like this much which results in soup tracks being duplicated.

To workaround this I just completely delete and recreate my soups each time I add tracks. It's a time-consuming pain to have to do this and forces me to batch up a lot of tracks before uploading to my empeg to make the ordeal worthwhile.

I'd be willing to pay a reasonable amount to have the "sort by track number in soups" code enabled.