Issues with AUTO mode

Ok, not sure what further information that will be needed. I have multiple APM boards. Currently have tried 2 in this Q450 and still have the same issue.
Have:
Calibrated the compass and GPS. (On separate board and traces cut as needed)
Wait for baro to warm and stabilize.
Copter goes through all the pre-arm checks without issue.
9 satellites before attempting to arm.

Have used the MP to upload a simple set of commands:
Liftoff to 15 feet
pause 2 seconds
go to WP1 (100 feet left) 20 feet hereafter as default altitude
pause 2 seconds
go to WP2 (100 fee right of home)
pause 2 seconds
RTL

So sometimes the copter just sits at liftoff altitude and does nothing forever,
sometimes it heads to WP1 and then does not pause, but goes on some secret mission that I have to interrupt and use RTL to get it back. I think only one time has it done the mission the way it was intended.

What further info is needed? And, what parameters should I check?
Thanks

Do you have any logs?

This file does show the last attempt

You can also see RTL went the wrong way.

Just returned from a different flight, with a cleared log first.
I recalibrated (again) Found compass setting off 180 degrees, and not as it had been, not sure why. Got that corrected. Put in new mission,
WP1 takeoff
WP2 50 yards to the right with a 5 second delay keyed in
WP3 was back in front of myself,
WP4 was land close to launch site.

Armed, then flipped auto switch, gave a slight pause then flipped switch for auto
Got liftoff and then just loiter at that point.

So flipped to Acro, and back to Auto. Then it went to waypoint 2 and stayed there.
Then I did RTL since it was still drifting away, and it did not hold any altitude even though throttle was adequate for slight climb.

Have included the log file.

Well my educated assistant on this has been tearing his hair out. He did find some strange things in the log file I guess, like the mag was off even though the parameters said it was setup.

Because of these types of issues, we both decided (at the same time even) that it was time to clear the eeprom.

Also of note, this is version 3.1.5, not 3.2, so I have this in the wrong sub category…sorry bout that. Move if need be.

Will try out in a few hours and see if issues are resolved

After resetting everything and doing a mission almost everything is right. I did have an event where it dropped a large number of feet before recovering, this looks like a barometer issue, will try putting the APM in it’s case and black it out. For now I will call this solved