After fiddling around some more with the settings, I found out that I had to use the option to configure controller on the main UI, to let Amibench “know” which port my mouse was using. A bit odd that if the UI knows there’s a mouse being used, doesn’t automatically apply that setting to everything…
Also, about the keyboard situation, when I configured the shortcut key to access the menu it identified my “help” key as “Insert”… that makes me think that maybe I didn’t chose the correct keyboard configuration on the initial setup. As a suggestion, on the keyboard menu there could be an option for “original Amiga keyboard” that maps the Amiga keyboard automatically. Then, we would only need to choose the layout and it would be ready to go.