Not sure how to get to the "multimedia > phonon > audio recording" setting mentioned above; but I managed to sort out my own particular issue as follows (and this might not be 100% related to the OPs issue, but there seem to be many people looking for such help)
I noticed that Skype was using my webcam mic, which is built into my monitor and too far away to be useful. I wanted it to use my headphone mic. It seemed hard to convince it to change. Eventualy, I ran pavucontrol, started a test call in Skype, which brought Skype onto the "recording" tab, and here I could see it was recording from the monitor webcam device. So I chose the internal audio device (basically, my sound card), and all was working well (if a little too loud, but that's easily solved, you never heard anyone complain their mic is too loud in skype!)
No idea why it's so hard to point an application at a different device, or maybe it's skype's fault for not using some sort of 'default' (though I don't see any concept of a default input device in pavucontrol)
HTH
http://askubuntu.com/questions/157931/ubuntu-12-04-replacing-pulseaudio-with-alsa
– Aug 02 '13 at 17:12http://askubuntu.com/questions/157931/ubuntu-12-04-replacing-pulseaudio-with-alsa
– Aug 02 '13 at 17:13