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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?

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Did you look at the source to see if thickbox JavaScript is included? –  Bainternet May 9 '11 at 20:56
    
and are you using 3.3beta? There is a known issue with 3.3 beta at the moment fixed in the next beta –  Tom J Nowell Nov 17 '11 at 18:30
    
I was using the current release version that was out when I originally posted this in May '11. –  Josh Farneman Apr 13 '12 at 16:28
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up vote 0 down vote accepted

Update: I fixed the issue myself. The problem was resulting from where I had removed jQuery output from the front end of my site (using my own version) improperly. It was not an issue with Wordpress itself. The function I was using to unset it removed it from the admin as well. I hadn't realized that some of the hooks that can be accessed in the functions.php file can affect the admin as well as the front-end.

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