I emailed URC and got a response to call their tech support line. For anyone interested in calling, the number is (800) 901-0800, Monday thru Friday between 9 am to 6 pm EST.
I did call and got a chance to speak with a tech right away. The short answer is that you need to delete the entire device if you're experiencing this problem and start over again with that device. I did try doing that and it worked for me the first time. I was finally able to fully program my remote.
I hope I don't fudge this too badly, but the tech explained that when you learn a command over a button, it doesn't erase the current command, but "stacks" the new learned command on top of the old. I'm not sure if that means the stack moves over to the next button and then makes that button malfunction or what. I didn't ask for an explanation why the button that was re-learned actually performs the command properly.
I'm really enjoying the remote now. The added buttons and the layout really help to make it more enjoyable for using with the Dish Hopper DVR. One great surprise to me was that the built-in code that worked for my Epson 8350 projector actually has a discreet off command! I looked a long time for a code on the web and never found one.
