If before in game, it does read from MQ2MyButtons_default.ini (same sections), but once in game it reads/writes to server_char.ini. Those defaults should be used for the toon if they don't have any in their ini. I could add a global flag, I will put it on todo list.
Renamed the MQ2Mybuttons.ini to MQMyButtons_default.ini and loaded in a character that never had it set up, and did NOT read the buttons, so right now, it's only reading from the main server_character.ini.