I'm not sure if this is exactly caused by Loremaster or if it is somehow a bug on my character but the following seems to be happening:
Trying to learn a language using the 16 Intelligence (3) modifier is not providing any progress, regardless of swapped books or how much of a language is spoken near me.
I learnt Draconic, Celestial, Infernal and Abyssal while not using the 5th loremaster language choice yet.
This would technically make me 1 language over the 3 limit if it is the issue and may be the reason I am not gaining any progress at all.
As per:
http://wiki.nwnarelith.com/Loremaster#Bonus_Language

These Loremaster languages should not inhibit the learning of additional modifier languages.
Regards,