Jordan,
This issue has been fixed in 3.1. The automapping feature was added in 3.0.2, and unfortunately had a bug where it didn't work if you used a custom database table prefix (not jos_). It was a stupid issue on our part, and was recently found for the 3.1 release. We've added non-standard prefixes to our testing suite, and this shouldn't come up again in other forms.
Thanks again, and good luck!