I changed my template a little so that it functioned more like a website and less like a blog. The homepage is a static page and the sidebar links are all hidden static pages (links to the pages in sidebar set up manually using the links feature).
The problem is that in IE 7 and Maxthon (haven't tested other browsers) the sidebar pages resolve to a 404, but in firefox (3) they correctly go to the page. If I remove the hidden attribute they show up fine in IE (see "case studies" which is in the sidebar and top navigation - hence not hidden)
I have the following plugins:
Enhanced WordPress Contact form
Filosofo Homepage Control
Google Analytics (by Semiologic)
SEO Title Tag
I have removed some code from various template (like removing the text when there are "no comments", and modified page.php so that recent blog posts show up in the footer of the pages. I kind of made it up as I went along so probably messed up something along the way.