I’m glad someone else is having this problem. It took me a while to narrow it down to the media_send_to_editor filter.
The issue I’m having is using Jared Atchison’s excellent Custom Metaboxes and Fields for WordPress library (it’s not a plugin, you include it in a plugin or theme). When using a “file” formatted metafield that calls the media uploader, if I try to insert a video, I believe it attempts to insert the shortcode instead of the file url.
Any help or suggestions for removing the JW filter just from certain field uploads would be great. I’ll be working to figure out a way around it too.