Sorry for making a second post, I didn't want anyone to spend time researching my resolved situation for me. Unfortunately, Cerebrus still moderates all of my posts :( so rather than wait, I decided to post a second topic to save anyone any headaches.
http://blogs.msdn.com/sburke/archive/2008/01/16/configuring-visual-studio-to-debug-net-framework-source-code.aspx the above link fixed my problem. It is strange however, that so many checkboxes would change their state when I clicked 'no', but whatever, it works now!
