Well I figured out why when I reverted the errors still occured. I had to edit the post and resubmit it for the error to go away. It seems that it parses the bbcode once when it is submitted and then uses that for all of the posts, even once the bbcode is updated later on down the road.
I only figured that out once I uninstalled the plugin, and deleted the files and the media was still showing up. I had to manually edit the post for the tags to appear instead of the post being parsed. I am not sure if that is by design, but I sure hope not. It has caused quite a headache on my end.

Just hope it gets fixed soon, we use the media code a lot.