Quick update - if I go in to task manager and kill the background JRiver MC server processes, then full functionality returns to WMC. Transport controls all work as expected instead of being intercepted. Probably not a MadVR issue but a JRiver issue where as long as the server process is running (to serve the library around the house) it is stealing control of some but not all transport controls. Play, pause, ff/rw all work but stop skip forward/back, and others don't do anything or cause JRiver MC to start playing content.
Second update - upgraded to 111, no change. JRiver is set to load library server at startup. Immediatly after restarting my machine and never launching the full UI, I can press the combo play/pause button on my keyboard and JRiver starts playing video in the background. You can't see the video, but the audio starts and MadVR appears in the system tray. MadVR indicates that JRiver Media Center is the media player and killing all system process for JRiver fixes the problem.