I have experienced this as well.
It is commonly known that the 3DS is region locked. What is not commonly known is that certain games, can also detect what region the 3DS is running and can automatically change language that is "default" for that unit. This is bad if the actual game does not have a language selection option.
This can be observed in games like Resident Evil (Both Revelation and Mercenaries) and Castlevania Mirror of Fate.
I think there's no solution unless we get a sort of 3DS firmware "region changer". There exists one but is currently not easily done. And could easily brick your system if done wrong.