I am experiencing the same issue. Its as if the center point of the mouse is mainly at the bottom of its limit, thus can not move further down. Once saw a quick fix was to reduce the resolution of your monitor to something a little less like 1680 X 1050. This worked but it was a pain to switch back and forth.
Also, got a second monitor. When I played again, same problem persisted but if I tried to move my mouse too far right (where my 2nd monitor is located) and click, this would pull my controls completely out of the game. I have to lift up my headset and click on the Squadrons program in the taskbar to reengage it.
