MTK is the old GPS unit, pretty much all the current setups use uBlox which is a much better (faster and more accurate) unit. I had a alot of problems even with uBlox when the M/W board was in close proximity to either a power distribution board or battery/ESC wires. Getting the board further away helped, the best solution is a remote compass chip as far away from the EMI as possible. The newest versions of the uBlox have the mag mounted on the GPS backplane board, I have a couple of these on frames that didn't work for squat with the standard compass chip on the M/W board.
Readytoflyquads website now has the Pro Black board without an onboard compass, it uses the uBlox with the remote compass chip. I have one setup on a TBS DIscovery frame and the performance of all the advanced functions is comparable to my other DIscovery with DJI Naza, I couldn't get it fly reliably with the older board and onboard compass due to the power and signal lines running through the lower Discovery frame plate.
Once that's sorted, make sure you have the correct magnetic declination set in config.h in the 2.X code otherwise it's still not going to work correctly, then upload to the board and make sure to calibrate the Accel with the multi on a level surface. I've found setting the low pass filter for the Accel under Gyro Filters in config.h to 42hz helps a great deal as well.
Ken