Skype has this really "great feature", called something like "allow Skype to control the sound devices" somewhere in the Options. You need to turn this off, then go into your Sound Preferences (in Linux), and check everything. As a guess, Skype muted your system sound.
No, my sound is not muted. The device has changed I tried to purge skype and tried a lot of solutions (This problem seems to be very common to linux users, but not connected with skype) and nothing seems to work.