In Coin-Op Full and Score Mode and in NES Score Mode you can access the key remap menu with the Tab key on keyboard. In NES Full Mode there is a settings menu at top of window for remapping keys.
You can click the link below to reset all settings to default. Should fix any problem but WARNING it will delete all save states and custom settings, resetting everything to default.
If the first option isn't working and you don't want to do the second or the second also doesn't work, then we can try to find another solution.