Pixhawk overloaded with master branch

When I compile the master branch and upload px4fmu-v2_default to Pixhawk, after it reboots it has the amber FMU B/E LED blinking rapidly. According to the documentation, this means that the CPU is overloaded. This does not happen with 1.6.5. Any suggestions on where to start to debug this? The serial console doesn’t even work.


I pinpointed the commit that is causing this and this led me to find that I’m not the only one with this problem.