In testing the Eleven Rack with Pro Tools 11, pretty much everything was working fine.
(watch the videos below to see this in action)
I was having a problem on my system that was not allowing me to embed rig settings in the track. After several responses, including from Avid Customer Service, it was confirmed that embedded rigs are supposed to work.
After much research I noticed that in my MIDI input devices, I had 2 Eleven Rack entries listed.
After relaying this information, Avid Customer Service was nice enough to check PT11 and the 11R with a fresh install of Windows 8 Pro. They said that they were not getting the "2-Eleven Rack [Emulated]" entry, they only had "Eleven Rack". (see video 2 to see solution in action)
They suggested that I check in Device Manager to see if I had any drivers that could be causing emulated MIDI ports.