My bad, I didn't test fully before posting.
OK, here's the quick (or long if you have a lot of custom languages) fix.
On each of the custom languages add the following eval script
Code:
perform hero.assign[Language.xxxx]
Just replace xxxx with the ID of the language.
The "No prereq..." will make the language a legal pick from the menu, and the script will add the necessary tags for character validation.