I get this when I create a new JIRA project. I am THE administrator, so I don't know what permissions I could be lacking.
It seems to set up the project anyway, but I'm suspicious that something isn't right and I won't find out until much later.
Permission Violation
It seems that you have tried to perform an operation which you are not permitted to perform.
If you think this message is wrong, please contact your JIRA administrators.