I don't use Premiere CS6 or AE but it seems there are isses with rendering out projects that include AE comps. Try a duplicate of the project and

remove the comps
Disable Neatvideo effects (denoiser etc)

You can also make sure you are running on high performance power settings

Just select High Performance profile in Control Panel \ System and Security \ Power

If all this fails try the software rendered and see if you get an improvement