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This isn't really of any particular importance, it's just a minor annoyance, it seems every time I press one of the function keys to change a setting (like switch a save slot), the program acts as if I pressed it twice. E.g. if I press F2 to switch between saves it goes from state 0 to state 2, or if I press F4 to change frame limiting it goes from Limit to VUSkip, jumping over normal Skip. Any clue why this might be happening?

your keys are sticky/not fully plugged in properly? not had that issue here, check your keyboard

make sure you have both pad plugins options set to the same plugin (pad1 and pad2 on lilypad if you're using lilypad )

That fixed it, didn't even bother setting up the second controller so it was to a different plug-in by default.

Thanks