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(Edited 3 times)

1. I remember a few other Linux users had the same problem, at least one can be found a bit further up in this thread. Don't know if he managed to find a solution.

It should automatically keep the calibration (as well as other settings) in Linux as well as on all other platforms. You can alter some values in the custom settings menu and see if those are being saved. If not, perhaps you can investigate so that there is no permission issue that keeps it from saving (I'm not familiar how these things work in Linux). (In linux I believe the Playerprefs are stored under "/home/your user/.config/unity3d").

Good thing that you at least managed to get it calibrated properly. As you probably noticed - if one axis is reversed, you can simply reverse it in the trim settings (Click "Calibrate Controller" on the main menu and then "Skip to trim settings")

My guess is that the whole thing has to do with the joystick drivers on Linux not being consistent in some way.

Some Linux users seem to have success using this program: https://github.com/Vantskruv/wejoy

2. In Windows there's a command line parameter -"adapter N" that can be used to select which monitor you want to run it. That only works on Windows though as far as I know. Hopefully someone who is more knowledgeable in Linux will be able to chime in.

( Here is a list of the runtime command line parameters: https://docs.unity3d.com/Manual/CommandLineArguments.html )

1/a. I only managed to calibrate it once when the two directions weren't mixed up, but it got messed up again when I started the program the third time.

1/b. It wasn't an axis being reversed (up is down, down is up), it was the two changed up (up is left, down is right). So there's no way to fix it on Linux at the moment.

1/c. I'll check out wejoy, thanks.

End result: I'm using my laptop instead, booting win10. Having loads of fun. I'm still terrible at it but in my defense I'm starting from Acro with high rates so it will take a while. Sometimes it clicks and I make a bit of progress and it feels awesome. I probably won't even try flying my quad for a few more weeks before I get the hang of the controls.

1b: If the automatic stick detection gets the sticks messed up, you can click on the little circle that you see is the correct one (instead of clicking OK) when going through the calibration procedure.

Glad that you are able to use it on your laptop at least. I'm sure you will find that any practice you put in will pay off later in real life flying.