It’s a very simple fix. Version 3.9 of WordPress incorporates a new version of TinyMCE. This new version (TinyMCE 4) no longer includes one of the functions required by Shortcodes Pro.
You simply need to edit the following file:
shortcodes-pro/inc/shortcodespro-overlay.php
And replace the following line:
window.tinyMCE.execInstanceCommand('content', 'mceInsertContent', false, shortcodeContent);
With this:
window.tinyMCE.execCommand('mceInsertContent', false, shortcodeContent);
I couldn’t understand why cdoo didn’t just post the solution to this thread. But then I found out he was asking for donations for this very simple fix.