Ran into this error today, running Skype 126.96.36.199. Most of top Google hits suggest removing lockfiles and killing your profile, but that seemed like an overkill. After some consulting with the developers, it turned out Skype locking mechanisms are also possibly influenced by browser processes that are launched by clicking URLs or in my case, clicking “Open Downloads folder” button. This fired up an “xdg-open” which in turn fired up “links2″ somewhere in the non-visible process space, beacuse I probably don’t have XDG fully configured for firefox in my fresh awesome-based setup.
One command to reveal such Skype lockfile-hogging processes is:
$ lsof .Skype/your-username-here/main.lock
If there is no way to cleanly shut them down, kill them and Skype should be able to login again.