I have a character who started with an Intelligence score of 13 and, as a result, one bonus language. Then he gained a point of Intelligence (due to age) and now PCGen is telling me to select his bonus languages. I don't have the INTBONUSLANG option enabled to allow selection of bonus languages after first level.
As I recall, initially the reminder told me to select a bonus language but if I clicked the + it wouldn't allow me to do so, because I had already selected 1 out of a maximum 1 bonus languages. However, after restarting PCGen and reloading the character, I'm given the option to select another language. So, this could be (at least partly) a persistence issue, maybe? Not sure.
What system are you using? (Pathfinder, 3.5, other)
I'm using 3.5.
When changing the age category on a 2nd level PC, I don’t have the message to select a new language.
But I do have a message if I reload the character, and can select a second language.
I don’t think language bonus are retroactive in 3.5 (they are in Pathfinder, like everything else).
The INTBONUSLANG rule is now respected in the UI for determining bonus languages. Pathfinder has been updated to default this setting to true, but you may need to update this in preferences if it is already cached.