Comment 3 for bug 670656

This basically has to do with the obtuse routing Pulse forces on its clients. Pulse attempts to remember the specific routing a client (audio application of some sort) has used in the past and when the client starts it will attempt to enforce this routing. From the description you provide it seems pulse thinks the preferred routing is from the internal sound source to the skype.

For now there is no easy fix to this. I would suggest you use the application 'pavucontrol'. This will allow you to see and change the individual routing in place for each active client and sound device.

Marking invalid for the sound menu but pointing it back upstream to pulseaudio considering the bug really does like with this pulse 'feature'.