Pixhawk 3.4.3 Not able to fly Auto Missions Properly

I’ve got a friend who is flying a quad copter with Pixhawk running 3.4.3. Recently the copter has had issues flying in any GPS enabled mode (Loiter/Auto). When he switches to AUTO, the copter begins to do the flight properly but along the mission seems to lose orientation and cannot fly the pre-programmed route properly. At points it stops and waits while in Auto as if trying to figure out where to go next. I believe it is an issue with the GPS/Compass module (from 3DR). Could someone please look at the attached log and let me know what they see? If you plot the flight in KML you can see that the copter doesn’t quite make it to the way-points and overshoots the flight lines. From what I see in the log, everything looks good but I’m not an expert.

LOG FILE is HERE -> https://drive.google.com/open?id=0B62edZ4l5_rOOVpFN0h5QnpLOFk

Thanks in advance for your help!2016-12-21 16-36-19.bin (1.4 MB)

i cannot connect to google drive… so i guess you may have compass ekf error?

No Compass EKF error is showing up…

how can i send the log to you?

You can use a free file sharing website and share the link to your file here. For example:
https://workupload.com/

you can upload when you reply the question. You can see a upload icon,just click it and upload the bin.

Here is the BIN file for the flight 2016-12-21 16-36-19.bin (1.4 MB)

studenblume, finally figured out how to upload it. The link to the file is now in the original opening question as well as in one of my comments/replies

It does look like the GPS velocity and position estimates become an issue after about a minute in.
http://ardupilot.org/dev/docs/extended-kalman-filter.html#extended-kalman-filter-interpreting-log-data
says that when EKF4 SV peaks over 1.0, the filter is not using the gps velocity data. The number of sats reported does dip in that area as well. I’m not sure if that’s repeatable, but maybe local GPS interference?

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agree with your analysis