Try setting that "Mouse" key(the one under "Analog" button) to anything far from your normal controls, and press it, hopefully it will activate your mouse control then.
Edit: oh and I tried actual mouse control for the first time and must add, go to Emulation Settings>GS Window and disable fullscreen on double click, otherwise the shooting will be really irritating.
Edit: oh and I tried actual mouse control for the first time and must add, go to Emulation Settings>GS Window and disable fullscreen on double click, otherwise the shooting will be really irritating.