My wife got me JRiver MC20 for a Christmas gift. I installed it and have not been able to figure something out.
When I watch a movie, Youtube, or Netflix, the sound is off really bad. I turn JRiver off and no sound comes out at all unless I turn it back on.
If I am understanding your problem description, I think what your issue is has to do with the installation of JRiver's new WDM driver.
JRiver's WDM driver installs in Windows Sound properties (see Window's Control Panel>Sound) and reroutes all system sounds through Media Center (MC). Usually this is an improvement, but if you have it setup this way, you can't completely exit MC or you won't get sound from your other programs outside of MC. I assume when you watch Netflix and YouTube your doing it from "outside the MC program" (if not, stop reading now, and disregard my comments).
If the problem is due to the WMD, you can go into the Windows Sound properties and set a different audio device to your "default" sound. Usually this will be the sound card on the motherboard (like "Realtec Digital Output", or whatever your computer uses).
However my thoughts on this would not explain why sounds are bad with Movies (which would be playing through MC). So maybe I'm totally misunderstanding the problem.