I also ran into this exact problem, and what MalexPrime suggested fixed it for me. I had to clear basically every axis input, the Mixture, Prop Pitch and Throttle axes and then reassign them. Once I did that, everything worked fine. Notably, once they worked right they could be tested from the settings screen, you could see the axis moving correctly on that screen, I didn’t need to keep jumping in and out of the plane to test it.
I have no idea why it worked, but it did. If you haven’t tried it, clear all of them out completely, then start resetting them, and hopefully that fixes it for you.