I've been feeling a pang of nostalgia wanting to play uplink again. So I went to install it and got the 16-bit subsystem error which I fixed. I patch it and run it and it refuses to accept mouse input, or so I think. I fire up the computer in safe mode and the game runs just fine (if it wasn't for the lack of sound I'd just play it in safe mode...), so I enable software mouse. When I run the game back in normally started windows, I notice that the software mouse is a good deal higher on the screen than my hardware mouse. This is all ontop of the problem, that windows refuses to move my start menu and the title bar out of the way of my game. here's an image illustrating the two problems

The red circle illustrates where my hardware mouse is when I have that server selected.