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Skid steering problem in automode

I have a boat, skidsteer with 2 blue robotics t200 thrusters. Everything is ok in manual mode. If I put it in auto mode, it heads to the way points like a snake (not straight). As soon as I flip it back to manual, it’s all good. Any ideas?

I @halim, this sounds like a common tuning problem, I’ve heard it before from other boat users. You will have to change the PID controller gains to fix this. Check out discuss.ardupilot.org, there are more rover/boat users there.