Okay. I got it working now. Turns out it was one or both of my custom taxonomies I had added on with my custom content type. I knew it had to do with my custom content types or taxonomies because, if I took them out and reset the permalinks, everything worked fine.
The names for these two taxonomies where type and year. I simply changed the names to media_type and media_year and everything is humming along just fine now. I guess WordPress uses certain names and you have to be careful what you use because it can break everything.