Try fastforwarding the guide list to 03/30/12 or even to a date in April, hit OK on your remote, and then try adding the stations back again. That's what worked for me.
Same thing keeps happening with me. I keep losing ESPN, ESPNews, and ESPN 2. It's happened with a few other channels, but for the most part once I add them back they have been staying. The ESPN channels will stay on for about a day, and then drop off. Other channels are dropping off too, but most of the time I'm not aware of it and have to go through my entire list to try to figure out which channels were removed. Is this going to be fixed soon??? Very frustrating.
I had this issue quite a while back with a Motorola QIP2500-3 SD STB. I would spend forever setting up my favorites only to have them changed a few hours/days later. Certain channels seemed to keep getting dropped more than others. Other channels seemed to keep getting added. I went several rounds with tech support until they finally found a solution. I believe they called it a factory reset (name could be wrong) and told me that it was the most they could do without replacing my box. It was a reset that wipes out all your settings and re-installs the software/firmware. So you have to reset EVERYTHING the way you had it before, but I haven't had the same problem again.
Hope this helps