Not only are the two names horribly confusing (Windows Media Center vs. J River Media Center), but I discovered an incredibly tricky conflicting bug between the two! For the past year or so, I have been running a Windows Media Center 2005 system in my living room. For this entire year, I have been stumped about my inability to use the Skip, Replay and Stop buttons on my official Microsoft Media Center remote - all other buttons work flawlessly. Coincidentally, I have JRiver Media Center 11 set to auto-start with Windows so it runs next to Windows Media Center on my monitor (Windows MCE is displayed on the TV).
After trying every Windows hotfix ever released, deleting and re-creating Windows remote settings files and even attempting to short and reset my actual remote (all suggested by this post:
http://blogs.msdn.com/astebner/archive/2005/10/24/484423.aspx), I found the final solution. JRiver Media Center's "media key mode" feature was intercepting the remote signals. After disabling this in options/general/advanced, my life has returned to normal peaceful digital bliss.
This is not a complaint about either product, but simply a discovery that I thought the Media Center world should be aware of. You should have seen the look on my face when I figured this out on a slightly tipsy night with my girlfriend this week. It seems so obvious now, huh?
P.S. This applies to any version of Media Center that features the media key mode feature. I have since installed MC12 and the fix still works.