If you set a bind to something like left alt and then try to change it to something else, it'll change to that key plus alt if the key you change it to isn't also a modifier. When any key has a modifier key, trying to reset the bind doesn't work. If you reset something with a modifier of left alt then it'll display as "Alt + Left Alt" and becomes unable to be reset. The only way to fix the issue is to delete the options.amecsapi.txt within your .minecraft directory - even resetting all keybinds within the controls menu does not fix it.

I have not tested it without controllable yet, and am unable to do so at this time due to not being at a computer that can run the game.

It seems like with Controlling installed, I have the same exact behaviours. I tried to disable Controlling mod, and then Amecs's key binding system started working properly, reseting just fine and easy to use.