No I was only running as I was playing. But I did have other windows open, though they were minimized.
I should add that I have recently purchased two new monitors, and am running in extended desktop mode - however I do have both Mame and Pauline running on the one desktop, not that I think that that would make a difference anyway.
It's odd that you should have troubles during playback when MAME is not the active window either. I'll admit I don't know the inner workings of Pauline, but there is a Windows API call that is probably used to work out which Window should be looked at - whether that window has the focus (is the current active Window) should be neither here nor there. I did see from the Readme files included with Pauline that it makes use of an open source OCR - so obviously if you put another window over the top of the game score it will cause problems.
I've been considering writing a very basic pace program to work with Android based mobile devices, and may yet still do it. Which has got me thinking about the whole "pace calculation" issue, but I think these ideas would be better discussed in another thread.