While installing custom firmware on a 3DS does indeed remove the software-based region lock, it does not account for locale issues. Locale is additional data that a game will often ask the 3DS for that includes the console's current language and software region. As an example:
The 3DS is a Japanese 3DS set to the Japanese language.
You attempt to launch an American cartridge.
The 3DS tells the game that it is a Japanese region console and would like the game to run in Japanese.
The game, being an English game, does not have Japanese on the cartridge and does not know what to do with this information.
The game crashes.
In some cases, games may successfully launch with an incorrect locale, but:
Games may display partially or entirely in the language of the console, rather than the language on the cartridge
Out-of-region DLC may not work properly
To mitigate this issue, Luma3DS allows you to specify the game's locale to allow the game to work properly. You may also use this feature to launch a game in a specific language without changing the system language (for example, if you want your 3DS user interface in English, but to launch a specific game in French). This page covers the various ways that you can specify a game's locale.
Before you start
You must enable the Enable game patching option for locale settings to take effect. To enable it:
Power off your device
Press and hold (Select), and while holding (Select), power on your device to enter the Luma3DS configuration menu
Scroll down to Enable game patching and enable it
If enabled, it will be marked with (x)
Methods
This method is generally the easiest, as it pulls from your title database and therefore does not require you to look up the title ID of each game.
If you don't already have it, download Luma Locale Switcher from here (direct download) and install the CIA file with FBI
If you choose to get this from elsewhere (e.g. Universal-Updater), ensure that you get the build that is marked as "NIGHTLY"
Launch Luma Locale Switcher (the Luma with translation icon)
Select "Titles"
Navigate to the game for which you want to change the locale
Set the locale to what the game expects
For example, if it's an American game and you want it to run in English, you should set the region to USA and the language to EN
Exit Luma Locale Switcher
The game's locale should now be correctly set.
This application automatically creates locale files from a predetermined list. This list is not comprehensive and may not include every game that is known to have locale issues.
If you don't already have it, download Luma Locale Region Auto Setter from here (direct download) and install the CIA file with FBI.
Launch Luma Locale Region Auto Setter
Follow the prompts on-screen
If your game is on the list, then its locale should now be correctly set.
You can also set the locale manually by creating a text file.
Insert your SD card into your computer
Navigate to sd:/luma/titles/
Create the titles folder if it does not already exist
Create a folder with the title ID of the game
You can get the game's title ID from here (cartridges), here (digital games), or from the FBI -> Titles menu
For example, Taiko no Tatsujin: Dokodon! Mystery Adventure's title ID is 0004000000190E00, so you'd create a folder named 0004000000190E00
Create a new text document and name it locale
With file extensions enabled, the name of the file should be locale.txt
Type the desired locale (based on what the game expects) into the text document
For example, if it's an American game and you want it to run in English, you should set the region to USA and the language to EN, so you should type USA EN
Save your changes
Remove your SD card and insert it into your device
The game's locale should now be correctly set.
Extra: Extended Locale Setting
Some games, most notably Tomodachi Life, are known to not launch with basic locale settings because they look not only at region and language, but sub-region within that region (e.g. a country/territory and/or a state). You can still set the locale of such a game, but you will have to follow manual instructions using Extended locale setting.