Can anything be done to get this Controller to work with JRiver?
First of all, I have the exact same Logitech remote as you, and it is all set up fine, so I can tell you that it works perfectly with MC.
I suppose I could leave the HP remote IR (the remote purchased from JRiver) in the computer and use the smart Controller IR transmitter, but that seems redundant since the Smart Contoller is plugged into my HTPC.
The hub must NOT be plugged into your HTPC !!You only plug the hub into the PC (via the USB cable) to make the initial set up so as to get the hub talking on your wireless LAN; after that, you have to
disconnect the USB connection from the PC. The Logitech remote control zapper and the Logitech iPhone / Android App talk via wi-fi to the hub, and the hub talks to all your home A/V devices (including your HTPC) by I/R. So, yes, you must keep the HP I/R receiver eye plugged into your PC...
Put the hub somewhere stand alone where it can "see" the I/R receiver eyes on your TV, receiver, Blu-ray player, HTPC, etc. (for example on the side table by your sofa) -- the only physical wired connection is the power supply.
In the initial set up you have to tell the hub about all your "Devices" e.g. TV, receiver, Blu-ray player, HTPC, etc. and for the PC you should indeed choose "Windows Media Center PC". And indeed you need to select the setting in MC to disable WMC Control.
EDIT: see this
http://www.avsforum.com/t/1468520/harmony-ultimate-smart-control-and-hub