Have you checked for mark-up or CSS errors? They often cause browser inconsistencies.
http://codex.wordpress.org/Validating_a_Website
I have been trying to go back through and see what I can do about the errors listed on the validators but am not sure where to start.
error report
When I go into the back end of and look through the .php files the errors don’t seem to be there.
I was able to resolve the logo appearing twice with some CSS but am now having trouble getting the font (matrix) to work in Firefox and IE