This reminds me: Do you have font sizes increased in Windows in the accessibility settings? That could potentially have something to do with the mouse being off.

It sounds like your desktop resolution is, in fact, not 2560x1600 in Windows. Selecting "Current Computer" will always set it to exactly what Windows is using for the resolution. And this would of course explain why your windows don't fit. You would need to go into the Windows display properties to set that resolution.