I have an installation of wordpress with the core wordpress files in a sub-directory as described here: http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory. I've also changed wp-content to just content and moved it outside the wordpress core directory.
Everything works fine except the media upload dialog does not load via Thickbox. It will load in the browser window and functions fine. So it seems it's just Thickbox that is not working. Any ideas on what I may have missed, or how to correct this problem?