Yay, this'll be done quicker than I expected..
Ok, SO, I'm using the Dark Blue skin, and it should look completely like this...

Note, the Apps menu's customization.
I check the Start menu, and it looks like this..

And I KNOW it shouldn't look like that. It should be covered completely.
Now I mucked with WindowBlinds, but I can't find anything related to the Start/Apps menu. I have no idea what to do in Properties. Though when I checked, it was set to "My Current Theme".