The blog is at http://www.creativeoptions.com/Blog/ But I think I've solved the problem - kinda. It appears that the new template update includes some of the widgets in its own internal system now. So removing the widgets got rid of the block that included the heads for the side bar sections that kept popping above my header.
I'm not keen on this option, I don't think I have as much control as I'm used to on how archives and such are displayed. But at least the ugly box above my header is now gone.
Thank you for everyone who spoke up to try to help.