After coming out of AUTO pitch / roll commands are wrong

Let me preface with I’m a NOOB. I’ve been playing with a F550 with a generic Pixhawk 2.4.8 running Ardupilot. I’ve had a couple dozen successful flights which exercises LOITER, ALTHOLD, RTL and AUTO. I should say almost successful as there is a glitch when transitioning out of AUTO. The issue is the right stick (roll/pitch) are wrong. They might be inverted but I’m not a 100% as I panic to get the thing down. Once power cycled all is well again. This is repeatable now and I transition to RTL only after AUTO and then nurse it in the last couple of feet with wonky controls. I upgrade from Ardupilot 3.x to 4.0.5 and problem persist. The radio is a FS-i6X running the firmware it came with.

I’ve tried to get a better understanding by looking at the RCIN data in the log, but without success so far. I’ve uploaded BIN to my Google drive here.

Thanks in advance for any help in resolving this issue.

It’s probably in Simple Mode as you have the SIMPLE parameter set to 1. If you want to use Simple Mode assign it as an RCx channel option and enable/disable it with a switch. Then you can use it with any mode.

That was my problem - I was in SIMPLE mode the entire time. I always started standing behind the copter so there was not much difference between simple and regular. When coming out of AUTO the orientation was changed and that’s where my problems began. Thanks for taking the time to look at the log!