I have a scratch built Hexacopter (Hobby King) with NAZA V2 Light Control Board and Futaba Tx/Rx. I am running 6 x NTM 28-26a 1000kv motors and Proflight-UK 30A Simon K ESCs. I am running 3 cell Lipos. (Not powerful enough, I know, waiting for order to arrive)
As soon as I take off, the model drifts to the left for about 10mts and then settles down. I have extended the post holding the GPS to 13cm to ensure there is no interference from the electronics within the body. I have also waited some 2/3 minutes to ensure the NAZA had warmed up. Although I can reduce the drift with trim, as soon as I change batteries, the drift returns even with the trim set for the previous battery.
I have calibrated the ESC/Motors and this does throw up an anomaly. I can calibrate motors 1 to 4 without any problem but motors 5 and 6 start up when the throttle is moved from high to low during the calibration as though they are reversed. Once the hex is set up ready for flight, motors 5 and 6 react the same as the other 4.
My first suggestion would be to ditch the NAZA and put on a pixhawk or ardupilot 
. As that’s what we prefer flying here (just my biased opinion).
But to help you with your situation, firstly is does sound like you are doing the correct thing by making sure the GPS/compass is far enough away from other electronics to avoid interference. To start my suggestion would be to make sure you are using the latest version of the DJI NAZA firmware. And also that you have gone through all the proper compass and IMU calibration steps through the assistant software, as the problem you are experiencing could be due to the z axis not being set properly… Also when you power on your NAZA V2 make sure that you dont have any trims set on your radio.
Thanks for the reply
I know what you mean by ditching the NAZA but I have another set installed on a quad which performs well. So I have decided on a plan of action:
Go back to the start and make sure I have the latest firmware etc and rebuild. If that fails, I would be tempted to swap out the system I have in the quad and see if that works or maybe a piece at a time to see if I can identify a particular piece of electronics that is causing the problem.