I have been having a similar problem with my Hopper for the last three days. Though the CBS programs that are set to record are fine, all programs on NBC & ABC are recording on their own, anything and everything, including news, sports and infomercials in the middle of the night. I do not have Prime-Time-Anytime set, nor have I ever used that feature. I thought that possibly things were erratic due to the time change, which usually happens with DISH scheduling, but so far it hasn't made any difference. Every day now I have had to spend 10 minutes or so to go through the schedule and skip almost every program. I had problems with shows that were not recording a month ago, and though it seemed like a software issue to me, DISH customer service had our Hopper replaced.
It seems to me that whenever DISH introduces a new feature on the Hopper, it screws up the reliability of the other features we have come to depend on. While I am all for introducing new features to stay on the cutting edge and increase DISH's advantage over it's competitors, there should be more beta testing among smaller (and willing) groups of participants to discover and correct these bugs before unleashing software updates on everyone. Or a way to rollback a software update to a previous version.