WP Super Cache causing logon page in a pop up on admin panels.

Everything else is fine. I am using mod rewrite on the server. Every hour a large pop up box appears on the admin panels, and displays the login page in the pop up. When I click the X in the top corner, the pop up reappears each time. Only when I login to the site via this popup box, will it go away. However, in any other admin panel I am working on, it’s business as usual.

I have checked my settings and I cannot see what it may be. It is this plugin, because I deactivated all other plugins, and this is the only one causing this issue.

What could be causing this? Which setting should I change?

http://wordpress.org/plugins/wp-super-cache/