This reminds me of another annoyance that was popping up on my machine - my game volume kept dropping right down whenever I tried to run Skype at the same time. After trawling through the Skype settings and finding nothing I eventually found that the culprit was under Sound in the Control Panel:
Nice Rythos, thanks. I'll just add to that if skype is going funky while streaming, there are also auto adjust settings in Skype that you might want to adjust.
I'll edit these into the OP as other potential fixes
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