Just an update guys. I emailed Jess the DEV and he is aware of the problem.
Here is his reply.
Yes, I am aware that WP Supper Edit is broken. I am currently reviewing updates to TinyMCE in WordPress and I will release an update as soon as possible. The WordPress core developers have made extensive changes to the TinyMCE integration code, so this may take me a while. The day job has kept me busy lately so I knew I wouldn’t make the WordPress 3.9 launch. Sorry bout the delay.
Thanks
Jess
Here was my reply back.
Hey Jess,
Thanks for your reply. Thank you for such a good plugin that is for free as well. You have done a great job and I appreciate it very much. I understand time constrains also and that wordpress changes things quite a bit at times. Thanks again for your reply look forward to your update.
Thanks,
Just wanted to give everyone on here an update.
Thanks again Jess for such a good and FREE plugin. It works great and I am sure you will get it fixed soon as you have time.