I wonder what the problem was (if I'd understand the answer).
To visualize the problem, imagine that the mouse cursor is visible on your screen while you are controlling your ship.
You start with the mouse centered on screen. You start pitching up by moving the mouse down. Your mouse cursor starts moving towards the lower edge of the screen while your ship starts accelerating upwards. Now you right-click the mouse to center the virtual joystick (which is the mouse itself) and the pitch/roll cursors. The ship stops moving and the two cursors are centered as the virtual joystick coordinates are zeroed. But the mouse cursor itself is still near the lower edge of your screen. Now, you continue moving the mouse down so that you carry on pitching up. What happens is that your mouse cursor now arrives at the bottom of the screen and stops there. Your pitch cursor has moved and you are pitching, but since there is no more room left for the mouse cursor to move futher down, it appears as if your mouse control has stopped responding. That was the problem you were experiencing and, because it obviously depends on the initial position of the mouse cursor on the screen, sometimes it seemed to work, some others seemed to work less and sometimes it seemed to not work at all and it was very difficult to find a pattern.
The solution is that now we are physically re-centering the mouse cursor coordinates when you right-click, together with the virtual joystick coordinates. This way we can ensure that the mouse cursor has always enough space to move about doing its business.