I just installed Ubuntu 8.04 and I set the /home to a separate partition, this /home is used also by Arch Linux. I think the problem may relate to this.

Basically whenever I try to run an application that requires gksudo, it claims my password is incorrect, however, when I use sudo in the CLI it works fine.

Yes it is the same user name in /home for both OSes. And ive made sure the user is in the group sudo.

Any ideas why this is so? thanks in advance.