This hasn't gone away for me either
It seems to have a random factor to it. When this first showed up with the 2.5.6 update, I was able to switch out of full screen set the mouse into the lower left corner, switch back and it worked. Now I've found that doesn't work. In fact switching to full screen makes it so I cannot even hit the EXIT for the game, as the mouse won't move that far down. Worse I didn't have a mouse cursor in the flight window.
This is like the old Nintendo cartridge voodoo. Start, stop, switch modes back and forth, start mission, stop mission, start mission...sometimes it works...sometimes it doesn't.