This script will fix the "There is another version of Skype running" error with out forcing a reboot.

FixSkype.sh

#!/usr/bin/env bash

# Tested on a mac with bash shell.

# This script will fix the dreaded "Another copy of Skype is running"

#First let's try and determine what PID Skype thinks is running and kill it, just in case

SKYPE_PID=`cat ~/Library/Application\ Support/Skype/Skype.pid`
kill -9 $SKYPE_PID

#Now, let's go ahead and kill the two files that Skype cannot clean up:

rm ~/Library/Application\ Support/Skype/Skype.pid
rm ~/Library/Application\ Support/Skype/shared.lck

#You should be able to restart Skype now!