Very interesting issue. In the short term I recommend either using the slow down modes instead of pause for that use case or building a combo by hand in the input editor (this is how I do most TAS stuff). I will look into this after the holiday. I'm not particularly good at umvc3. If you could give me a zero input sequence with some times where you want pause and unpause to work it would help me look into it. Did you try using the keyboard hotkey for the pause and unpause? Not alt/tabbing to swap the game in and out of the foreground may work.