That's because the resolution has to be changed, it's finnicky and the window has to be redrawn with the new resolution.
I don't have an exact method, but change the resolution in the settings to something different then change it back, toggle between full screen and window.
You have to get the window to "redraw" on the screen.
When you finally get it it will all be working like you want it to work. (You will be able to click where your mouse is pointing.)
I know your issue exactly, the better way is if you can tell the game to launch on a specific monitor, or even mirror your monitors. There are lots of guides online that demonstrate this procedure.