I tried working with all 3 versions of pandoc I had installed appearing as system("which pandoc"), and all of them didn't hang. All returned immediately. Unfortunately, I still see the rsession hang followed by pandoc hang. The latter of which I can kill with pkill. So, I'm pretty sure it's not pandoc's problem.
Also, I've polled people around me who are also using this server and only one other person had R hang on them, but I'm not sure it was because of this issue. Could there be something special about my session that could cause this? Could a build up of temporary files cause this?