I opened a ticket for this already, but I just wondered if anyone else experiences it....
Often as I'm playing, the game window will seem to pop out of focus. I see the game mouse cursor is replaced with the standard windows pointer. In this situation, I'm still in control of my ship via my XBox 360 controller, but I've lost keyboard input (typing results in the 'system ding'). The only way to get back is to click the mouse, which minimises the game window and drops me to the desktop. I can then re-focus on the game by clicking the icon on the taskbar.