I'm going on a long shot here but I found that the error_reporting(E_ALL) function is causing a fault in not just the media manager but in plugins using Ajax OR plugins that have their own media button.
Not done enough research to know the specifics but I found that removing error_reporting(E_ALL) fixed a plugin that was returning NULL during an Ajax operation and removing the line stopped media manager from indicating an upload upload failed despite it actually uploading.
Again that indicates Ajax returning null at some point.
Rather than spend more time looking into it I thought I bet get it posted as there seems to be an increase of popular plugins failing that normally have no issues.
I also posted about this already but in regards to the media uploader as that has been raised a lot. To get peoples attention to the issue who are seeking help with a plugin I created this post.
I may be wrong on how severe error_reporting(E_ALL) is but I suspect WordPress 3.5 has a bug in an Ajax function.