Update: It was a clean install. The only thing I had done was add/hide some content web parts on the default page via the UI. So what I did then is simply mark the install complete to "false" in the webconfig, created a new database, and ran the installation again (with the same codebase). With this completed, the problem simply went away. I don't have time to try and recreate it. I'm just hapy it's working fine now.