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?

Have you gone through the tuning steps as outlined in the links here:

This can be quite difficult and requires great patience but it is absolutely necessary.