if this helps at all, it's not resolution or aspect ratio sensitive even it will just map x and y to 0-1 then project it onto the target window if you like...

I don't use the click stuff but im' not convinced it's a problem with my app yet 8)

it seems to work correctly to me

maybe, your second instance has a binding to alt+whatever key somewhere. even some mods can steal the binding even if they aren't loaded in my experience.