I brought out my quad for some Spring flying. Did a few tests of pos hold, landing, and basic flying to see if the it still worked after the long winter. All worked fine. The copter held well in pos hold and I could fly it around with no issues.
I loaded up a simple mission planner mission and sent it out for a run. While on the mission in Auto mode, the copter at time flew really rough with large oscillating swings during parts of the flight. Looking at the log, you can see exactly when these happened by looking at the RCOU.C1, C2, C3, C4. As you can see it happened at different parts of the flight.I actually decided to land it in a field as I was afraid it would flip as the swings were that extreme.
The only changes from last fall is I loaded on my pixhawk Copter 2.4.6 and bought some new CF props. I balanced the CF props. The frame is a F550, 9443 CF props, PixHawk controller, and 2212 940 KV motors.
Here is the log file: https://drive.google.com/open?id=0B8-ATMPoKFG6Yk12U1RjNC1MVjA
Is there a motor or controller issue? Or does the Copter 2.4.6 have an defect in it?