Still happening this morning, except it was going through periods of behaving fine, or some channels going out but not others.
So, while I was at work, my girlfriend got fed up with it and called Dish. She says that at first she got a recorded message saying that they were having problems with certain channels. But she talked to an agent anyway, and they told her that there was a compatibility issue with certain DVRs due to some changes they made recently! Supposedly they're working on it.
It seems awfully strange to me that nobody is complaining of any such issue here (although this last Hopper software update introduced other bugs, such as the Joey compatibility issue.) Also, the impression she got from the agent was that the compatibility issue was hardware-based, because we just Wednesday night activated a new Hopper to replace one with a bad hard drive. (I did notice at the time that activating the new Hopper took MUCH longer and MANY more reboots than the original one did! I now wonder if there was any connection between that and the alleged signal incompatibility issue.) Also, the problem started, as far as I can remember, the night BEFORE I got the new Hopper, although we were having sleet that night so I thought maybe the weather was the cause then. (But on the other hand, I think my new Hopper is the same variation as the old one -- the software version on both ends in "NDGD", whereas I've seen other people on here say that theirs ends with different strings.)