The firmware for version 0.5 became default in the git repository. If you pull updates from git and have a version 3 prototype, you have to change firmware/axoloti_defines.h
//#define BOARD_AXOLOTI_V03 1
#define BOARD_AXOLOTI_V05 1
into
#define BOARD_AXOLOTI_V03 1
//#define BOARD_AXOLOTI_V05 1
before compiling and flashing firmware...