I recently updated my Ubuntu setup, which involved upgrading to 14.04 and also moving my monitors/laptop screens around. An unwanted side affect of this was that when I was receiving an incoming Skype call I wouldn’t see the usual popup alerting me. This meant that although I could hear the ringing, I could not answer the call. The issue was that the popup was appearing off screen rather than it not appearing at all. A quick search led me to this post on the Skype forum that mentioned a solution through modifying the ~/.config/Skype/Skype.conf file. This file (or mine anyway) contained lines that look like this;
[IncomingCallPopup] position=@Point(58 400)
By modifying the values I could easily adjust where the call notification would pop up. There’s also a handy Test Event button in the Skype Options tool which means you can simulate the incoming call to see where the popup appears.