Hi, there are currently two ways to disable this. One way is to set the modifier key to something else, or even nothing, like this:
modifier_key = 0. There’s no UI for this, so it has to be set in config file / custom config in FS-UAE Launcher. Another way is to use the key combination Mod+K (aka Cmd+K) to toggle full keyboard emulation during emulation. Read more about it here: https://github.com/FrodeSolheim/fs-uae/blob/master/docs/keyboard.md.
What’s missing is the ability to use full_keyboard = 1 to set the initial state for the full keyboard state. This will be possible in 2.7.5.dev 