CMS Template works when site disabled, but not when enabled
 

Hello folks

I recently installed suite 4.0 and its coming together slowly, but surely. I've ran into a couple problems trivial to your experienced user so far (i am not), but other than that its coming along somewhat smoothly. I'm just trying to get things operational before tomorrow.

With Internet Explorer
My problem is weird and I don't understand why this happens, but when I disable the site and go to the URL of http://www.fragdods.com/content.php it shows up correct (screenshot}. Then when I login the front page is messed up (screenshot), but the forums look good (screenshot). When I enable the site the front page looks messed up again (screenshot)

With Mozilla Firefox
It does basically the same thing as IE8, but with a completely different template. I'm dumbfounded by these issues, and have no idea where to start to clear it up. If anyone is familiar with this issue I would appreciate any help given.

Happy New Years!