Obviously I have Skype running on my Vista partition but trying to login to skype in Linux I get that message.I dual boot with both Vista Ultimate x64 and now Ubuntu 9.04 64 bit so how do I login via Ubuntu without getting that message?.

Hello,
from here:
http://forum.skype.com/lofiversion/index.php/t93885.html
Try this command in a terminal (replace user by your login name ):
sudo chown user:user .Skype

You can also try to remove the .Skype directory.
good luck