I took this picture of the full window chrome in Chrome so that the juxtaposition of the banner across the page shows. I've also included one from math.se (where I knew I wasn't recently logged in) to show the juxtaposition. I have always had this issue on StackApps that I can recall.
While I realize this isn't HIGH priority to be fixed, I am curious if others see the problem (for vindication that I'm not losing my mind) and if I recall correctly this is because StackApps doesn't run the "standard SE2.0 setup" (and wanted to verify that).
So in other news ... I'm curious about this SE2.0API beta ;-)