There is something wrong with timers on Windows when the mouse cursor is outside of the window.

See the attached test application.

The program is simple, it uses thread-to-thread messaging to update a counter, displayed in the window. You should run it with the cursor entirely outside the window boundaries. The test is also simple, the counter never stops, so if it does, then it's broken. If the counter restarts as you move the cursor back into the apps window area, that's the bingo - a message was stuck, due to a failed wakeUp(), and the mouse message got the pump moving again...