I think I'm having a very similar if not identical problem... Mission Control worked great for about a week and then out of nowhere the top section with menus, user info, MC logo, and what not turned white instead of grey and all the text up there turned black.
Can you explain how to fix this? I don't know how to change the permission for the above php files.
Can you explain how to do that? I don't know anything about php. I opened said files in Dreamweaver but didn't see anything about permissions so I'm assuming I have to do something totally different. I'm kind of a noob... sorry
Addendum for future troubleshooting -- I use Akeeba Admin Tools, and the default settings for the .htaccess maker prohibit the use of PHP files that are not /index.php.
I had to set an exception for "Allow direct access, including .php files, to these directories";
/administrator/templates/rt_missioncontrol_j16