I guess this is more of an FYI than posted with the expectation that anything can be done about it, but when Shortcodes Ultimate is active, the edit window WP Editor (where the code is) displays below the list of files rather then to the left of the file list. So you need to scroll down to see the code.
Also, a warning about changing views without saving is displayed when a new file is clicked, after entering the WP Edit, even when no changes have been made to the originally displayed file.
That aside, this is a great plugin. Much easier to work with than the WP default editor.