Okay, this helped me better understand the control config issue.
So what I think is happening is:
You are pressing buttons on the controller, which in turn activates the input in game, but then JoyToKey converts that input to a keyboard input, which in turn also activates in game causing a sort of loop and therefore switching control scheme between controller and keyboard since they are separate.
That's the only explanation I have for it switching control schemes by itself without your input.
So the solution(s) would be:
1. Since the game detects the controller then just use the controller without JoyToKey and bind everything in game, this is of course if the game actually understands the SNES controller, I have no idea about that.
2. Disable controller detection completely with the mentioned "controller enabled" option, this should make it so the controller does nothing to the game and all inputs should be keyboard only, which in turn *SHOULD* make JoyToKey work.
I think I will add a message in the controls menu recommending people to disable controller detection if they are planning to use JoyToKey.
About the suggestion, if I'm not misunderstanding then that option basically already exists, but without the "stop moving" part, since there are dedicated buttons for aiming and not just using the directional keys.
Sure, music is pretty important but exactly as you said, it's not really a priority right now, the priority is actually finishing the game and fixing the most glaring bugs.
Yeah, that's what I thought, the font couldn't be THAT bad. ;) but as mentioned before, hopefully I will fix this issue when I add support for using a more standard font, not sure when this is coming though.
As for the graphics, my suggestion would be:
If the shaders are not auto disabled eg: shows a message that they are "not compiled" and the button does not accept input, then:
Try using the "Low" or "Medium" graphics preset with the "Frame Skip" option turned on in the "Display" options.
This might allow you to play the game with some graphical things turned on.
Also, to be honest here, I haven't really tested the game on Windows 7, but it should work the same as on Windows 10, all I know is there are definitely issues running it on Windows XP that's why I put Win 7 as Minimum Requirements. :)
Anyway, thanks for the extensive reply since it (hopefully) helped me find the cause of the control issues.
Also, it did not really seem like you were trolling me or whatever, you said what was wrong and that is what I expect from feedback. :)
(sorry again for the "wall of text" reply)