I was speculating the same over on
How many times do you have to calibrate the compass?
specifically that the FC Yaw value wasn't initialized correctly. It was further speculated that it was related to the FW version. But, I don't think so because these incidents have occurred using FW dated Feb 8 2018 (@Helgegustav ) while other other flights using FW dated Feb 8 2018 didn't have a problem.
Just spit balling here. Is it possible that incorrect Yaw initialization happens when the MA is powered up while being moved about by the pilot? (Shouldn't make any difference; I do this all the time with my MP) If there is a slight delay between reading magYaw and initializing Yaw this could cause the error. OTOH, a stationary MA wouldn't have the incorrect Yaw initialization problem. The .DAT from the MA itself would show if this happened for these incidents. Unfortunately, the tablet .DAT doesn't have initial 1 or 2 secs of data required to determine this.
Maybe. But one other question to throw in with that - why do the two IMUs end up initializing at such different values? Slightly different initialization times perhaps? And also, once initialized, as the aircraft is further moved around, why do the rate gyros not update the initialized yaw values accordingly, as they would do in flight?
So another test might be to deliberately power up a MA while rotating it to see if that leads to this effect.