When playing on a laptop with the laptop's trackpad or trackpoint the mouse cursor is not captured by the application.
In windowed mode, the mouse cursor goes out of the game screen, clicking make the screen lose focus and the game is paused.
In fullscreen mode, the mouse cursor hit either the hidden application title bar when going up or the windows taskbar when going down. Any clicking on these will have the same effect as above.
This basically make the game unplayable.
I've found that the cause of this problem is the SynTPEnh.exe process on my Thinkpad laptop. Once killed all mouse issue disappear.