To my knowledge the only custom things added were some social networking controls. Compression is off and view state was not disabled.
The only URL rewriting is the default items in the web.config. Nothing should be altering the requests to my knowledge.
I used Firebug to view the request/response from clicking on the administration area. The request goes through but the response comes back as a 302 Found, but the location is incorrect (it returns the redirect page, instead of services.aspx). Under response here is what the message
ailed to load source for: http://cfs.wisc.edu/Sitefinity/Admin/CmsAdmin/Services.aspx"
Don't know if that gets us any closer to an answer at all....
Also, I really feel like this has something to do with the failed Search index creation I mentioned. As the ONLY time this seems to happen (at least the administration area part) is when I go to create a new search index for the site. In fact, this seems to be the case as I can get to http://cfs.wisc.edu/Sitefinity/Admin/CmsAdmin/Services.aspx?service=RSS+Feeds and create a new feed without issues.