I noticed a problem in the way the script admin/tinymce/tinymce.js that handles the shortcode popup of TinyMCE editor, inserts the code in the editor area.
The script looks for an editor instance named "content" but this does work only for pages/posts content areas, and not for other editor instances.
In example, I made a plugin which uses TynyMCE editor for widgets content, and the NextGEN button/popup doesn't add the code to the editor, because of this. I'm pretty sure that also other plugins using TinyMCE instances are affected in the same way.
Please could you change this behavior, and let the shortcode be added to editor instance which opened the popup?