I found that when I remap keys I have to remap them on both pages of the controls options window.
What I mean is when you're on the controls options page in the top left there is a drop down menu, the options are a10 sim and a10 game, I have no idea what they are both for but I changed the options in only one of them and it only affected some of the missions I was flying, so try changing them both to match each other and see if unpausing works then would be my guess.