I apologize for necroposting, but I'm having the same issue and editing keybinds.conf manually has no effect, the keybindings still do not work. I'm on Arch Linux and installed with the AUR version of 'mcomix'. I changed keybindings.conf and when I open the keybinding section of the menu, it appears that it recognized my change, but the arrow keys do nothing in the actual comic reading.
I apologize for necroposting, but I'm having the same issue and editing keybinds.conf manually has no effect, the keybindings still do not work.