The media library URL (/sitecore/shell/Applications/Media/MediaShop/default.aspx) is being picked up by the SiteCore handler and redirected to the page-not-found page Sitecore uses (/sitecore/service/notfound.aspx). The file is a physical file and is actually there. I've seen things like this happen with items in the Sitecore content tree, but not with physical files. Any ideas where to look would be appreciated. Thanks.
Update: So, the issue as described above is fixed, but it's clear that there are other problems, seemingly also media related. This file: /sitecore/shell/applications/media/mediafolder/mediafolder.js is showing the same symptoms I've described above. They file is there on the server, but Sitecore is redirecting to it's 404 page.