Hey,
I know this is an old thread but I had the same problem on two different computers (my Kubuntu on a 64 bit PC and my Ubuntu 10.10 running on my Acer One), both with Pulse Audio.
I spent about a week tweaking on it and I fixed it. thru no help of anyone whatsoever. While everyone had bright ideas that seemed to work for them, none worked for me.
Then a week later, I was poking around the skype forum and someone was using pavucontrol to adjust his stereo output. So I did the standard sudo apt-get install pavucontrol. Then I gave it a whirl and caught something evil.
On my Acer One: If you run pavucontrol and go to input devices, it sees my microphone as a stereo input. I noticed when I 'unlinked' the left/right channels and turned the RIGHT channel all the way DOWN, and the LEFT channel all the way up, the microphone instantly started working. Skype fixed.
On my Kubuntu PC: Whenever Skype was up and running, pavucontrol detected Skype was trying to use the microphone jack for a source and not my Logitech webcam mic. So I clicked on the button and changed the source over to webcam mic. Problem was instantly fixed.
While the Ubuntu Linux Gods found this problem uninteresting, I hope this posting will one day help out another of us little people.
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