Did you try rebooting just the Super Joey?
I hadn't since the 2 tuners being tied up with this crap were on the Hopper. Now I've tried that and no help, but after the SJ rebooted, it only showed one tuner on the Hopper and didn't show the other two at all.
So now I just reset the Hopper again to see if the combo would fix this for tonight.
This is weird. After the Hopper reboot, it shows 2 tuners on the Hopper, one I'm watching, one 'available' and Tuner 3 is shown as on the SJ and doing PTAT.
OK, while I was typing. All 5 tuners are showing up and all tuners are either available or recording.
At this point I don't know if it was the SJ booting that got things started in the right direction, or if it was booting the SJ and then booting the Hopper after the SJ finished its boot.
Regardless this is a serious problem and needs a serious and quick fix from Dish.
As an aside, this may be trying to tell me something. I've got both services now and am in the process of deciding which I'll keep. This next week will tell the tale.