Any ideas what the problem(s) might be?

Yes. This:

I'd saved up a bunch of new toonage, bumping me up from 40 to over 50GB (10427 tunes altogether).

The FAQ entry is here, specifically the third paragraph.

If I recall correctly, you might be able to fix it by cleaning up the tags. This is fuzzy in my brain at the moment, so someone correct me if I'm wrong, but...

1) The database size is determined by how much data is in the tags. So for instance, if all of the tags have their comment field filled out, the database is bigger than if the comment was blank in all the tags.

2) Dapper Dan says he uses iTunes to organize his collection. Doesn't iTunes put the useless text "Encoded with iTunes x.xx" in every comment field?

Perhaps it's as simple as removing the comment tag from all the tunes and reloading them. You might even be able to do that directly within emplode or Jemplode, but I have no idea how slow those programs will be if you try to group-select and change 10,000 comment tags. It might even crash the program to try.