Sorry for the week-late reply, and no they weren't cutscenes, unless loading screen counts.

I have encountered this issue on some of the game I played, particularly of those during the loading screen the game would flash my desktop content for a split second, or the game that changed screen size (ex. becomes full-screen when game loaded). The HUD would always turn from red to blue whenever...

So you're basically telling me there's no better solution? System sound or microphone sound, one of them is bound to disappear?

I recorded all my videos in AVI format, and in the setting I selected the "Record microphone into separate audio track". The problem I'm facing now, is that when I exported these videos, my microphone sound would disappear when they're converted into MP4 format. I heard that separate audio track won...