The "Things to be Done" area has a message "Select Bonus Languages" even though the House Rules option to allow bonus languages after first level is off (the character, a wizard, has focused on INT gains...).
A second problem with this is that there are no bonus languages left to choose from, the others being already all chosen.
I replicated this with a re-do of the character using a current 6.01 autobuild. Now the "Things to be Done" does not (immediately) have the message about selecting bonus languages but when I click on Add Bonus Language it adds selections as the intelligence modifier has gone up. The message appears, though, when the character is saved, closed, and reloaded.
The 6.00 release reads these characters as having bonus languages despite the preferences, but I didn't make another set from scratch.
The files are Garedon 01 (first level, no bonus languages), Garedon 08 (8th, +2 Int, 1 bonus lang.), and Garedon 17 (17th, +4 Int, 2 bonus lang.).
This is still true for 6.01.02 as of the Autobuild #174 (Mar 31, 2013 11:24:28 PM), rev. 19802. (Just trying some old JIRAs and seeing if they are still true.)