Sometimes other programs will 'hog' the Tuner card. I had trouble with MediaPortal when I installed it because its TV server kicks in on boot and *any* other DVB program couldn't tune any channels. I had to do a full uninstall of MediaPortal before things came back to normal. I've not used Wndows Media Center more than about twice and it was before I started using tv in JRiver, so I can't really comment on whether WMC has a similar 'hogging' of the tuner card. It has a TV server aspect, so it may.
Try rebooting the PC and then tuning channels in MC before you do anything in WMC. I find that sometimes a complete shutdown and restart rather than a soft restart helped. This resets the tuner association.
One time after I did a clean install of JRiver it failed to find channels, but after I played a video in it, suddenly it found channels again. I'm not sure about it, but I think MC tries to silently play the channels to get more info about them during the tuning process (ie it builds a filter graph whilst it tunes). I'm not sure whether the filters it needs to do this are downloaded automatically on first install or whether playing the first video does it. Like I said it only happened once, so I thought it was random.
I've disabled WMC in the Control Panel options, so I guarantee no Microsoft interferance in JRiver MC!
If you still have trouble, keep posting, we will get it working for you!
Cheers - and welcome to the forum!
SBR