In 6.01.03 autobuild #239 and in 6.00.1 RC3 (which I can't seem to find in the version list above), there is some odd behavior with the Gnome racial trait Gift of Tongues and its ability to give two languages per point invested in Linguistics.
[...trimmed extra steps, see DATA-1124 ...]
Upon saving and reloading, there is a bonus language available from both the intelligence-based “Add Bonus Language” and one from “Add Language via Skill Points”.
In sum, a gnome with Int 14, the Gift of Tongues racial trait, and one rank in Linguistics is 1) getting a total of 5 bonus languages, instead of 4; and 2) not getting these in the times and places expected during the character creation process.
(Actually, even more confusingly, I just saved and reopened the character and made the sixth selection, closed and reopened and made the seventh selection...)
Attached is an example character.