The only way around this problem i found was to uninstall and then re-install Skype.
Then remember that when you have finished setting up Skype or just finished using Skype always click on "exit" to make sure that another instance of Skype is not being loaded.
Don't forget that you and every other Linux user are paying the penalty by having to use a version of Skype that is outdated or still in beta mode with very little prospect of the software ever being updated and all because you choose to run a Linux OS.
That works if there really is another one running, I've just installed it on XUbuntu though, it was launched with LD_PRELOAD=/usr/lib/lib4l/v4l1compat.so skype.
Now, even though there is no instance running (nothing in ps aux | grep skype) when I try to sign in I can the "There's another instance running" message.
Had the same annoying problem. Found this easy solution (no unistall required):
These are all wrong.
Though I haven't found the way to overcome it, my workaround is very simple:
from terminal run -> sudo skype &
It logs in as root. All functionality is good.