A lot of roms feel like they have a longer delay between the button press and the action happening on the screen in certain genres. It's only a slight difference, but when you have a lifetime of experience on the cartridge and and switch to the rom, it can mess with your instincts and take adjusting to get used to. One example I've certainly noticed it on is Mario Bros. It's happened with both keyboard and controller imput on various computers spanning the last 20 or so years.