Ran the generate.py script in libraries/GCS_Mavlink as a test before trying to add a custom message and it breaks the build of px4-v2 by generating a different version of mavlink_system_t in mavlink_types.h. Most of the fields that are in the checked in headers are now missing. Not sure if this in the only error, but mavlink_system_t.type field is used in system.pde.
Easily fixable? I have yet to find where the instructions for generating that struct might be defined.