I'm using 12.04 64 bits and Skype version 126.96.36.199 released yesterday ( http://blogs.skype.com/garage/2012/07/hotfix_for_multiple_skype_clie.html ).
The problem is : I'm using Skype normally. No problems with that. The problem happen when I try shut down Skype. Apparently works, but if I check( ps -aux on console ), the instance still alive.
So, If I shut down and start Skype again I receive one message error : "Another skype instance may exist".
Someone knows anything about it?