Clean URLs and Popup Alerts
Any Javascript popups that load new pages are 404.
When viewing a "clean" version of an article, that is where the filename appears to be a subdirectory, the browser looks for all relative URLs in the imaginary subdirectory. This becomes a problem when JavaScript opens windows for viewing individual posts, IMing users from their comments, getting PM popups, etc, while in this particular view.
We have some work to do in terms of redefining a bunch of these JavaScript functions so that absolute URLs are used.