I am having a similar problem, and it's been going on for months now. I finally called Dish on Friday and received the usual "reboot your receiver" crap. While I know that did not do anything for me, the signal wasn't dropping out at the time and so I couldn't prove to them otherwise. I have a VIP622 with locals through the dish, not OTA.
Interestingly, the problem seems to affect my CBS and ABC (WSB) affiliates the most. I very rarely see any problems with Fox (WAGA) or NBC (WXIA). It was very frustrating trying to watch Lost and Desperate Housewives this past season, but 24 and House were rock solid. It's good to know that other people are experiencing the problem. Perhaps if enough people complain they will finally do something about it.