When I run both Skype and Rhythmbox, Rhythmbox is paused every time a Skype notification arrives (on receiving a new incoming message, new file transfer request, incoming call, etc.). I find it quite annoying.
There are at least 2 ways to resolve the problem I've come across:
1) turn off all Skype notifications - and Rhythmbox is never paused. However it's not a good solution at all :)
2) edit the default.pa file in /etc/pulse/
sudo gedit /etc/pulse/default.pa
and comment it:
# load-module module-role-cork
Log out. Login. Voila.
P.S. The OS used was Sabayon, I've also noticed the solution applies to Fedora as well.