question regarding theme and activation page

using the old version of edu clean theme, I just noticed that the page where a user activates his blog looks borked. I have used plugins to hide some of my pages from automatically being listed in menus and have manually included them in the footer. But it seems that on the activation page, plugins are not active or being ignored?

can I somehow change this template or otherwise prevent all pages from showing and overlaying my logo?

Please see screenshot: http://screencast.com/t/MDE1NTlhYz