Thanks for bringing this to our attention, we're aware of the issue and working on a fix.
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While you're looking at the pause code, please consider (for a later update atleast) a further improvement by giving a(n optional) pause key that does not have an unpause function. That is, separate pause and unpause (or pause/unpause) keys. In the current system (before this bug) I often press space to manually pause the game, only to find that a popup appeared a millisecond before my keypress, the popup paused the game and my keypress unpaused it again.