Random Instability During Auto Mission Flight

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?

As 3.4.6 is the current release and we are getting close to 3.5, I was wondering why you are running 2.4.6?

Did you mean 3.4.6?

What version did you have loaded previously?

And yes, there were significant changes in the 3.4 release.
So you may have to do a whole auto tune and setup.
I assume you did a fresh compass cal?

Mike, correct I was using version 3.4.6. I was running 3.3.3 all of last summer and fall. I did do a retune of the rig after I loaded the firmware. I did not change the PIDs with the new firmware. Would not updating the PIDs have had this effect? Can you tell anything from the logs?

A little confused?
You said you retuned the rig?
Did you do an Autotune?

Looking at just the ATT values of Pitch and Roll you can see the oscillations increasing and the divergence of Desired and Actual increasing.

I think you need an autotune but check the aggressiveness of the autotune settings.

Thanks for your help. I will try to go out and autotune again to see if it then behaves better. The forecast is for rain/snow this weekend so it might be until next. I will report back what I find.

I finally got it this weekend as the weather was nice. Autotune again with 3.5 rc 5. That solved my issues​.