I'm having this problem - but (so far) with only ONE show; "24". All the other OTA timers appear to be OK (again, so far). I have HD priority set (because we want to record the networks HD feed & is much easier for the family if they're all at the "real" channel numbers).
Tried a number of things to debug this. Found that 24 was at the top of the priority list, so I moved it down - next day, 24 timer had still disappeared. Tried deleting & then resetting the timers - next day, 24 timer had still disappeared. Finally went ahead & changed it to the Sat HD ABC local just to make sure we get it this week. Now I've got to monitor the other OTA timers - I'm expecting a different one to start disappearing now.
Dish - fix this! This really sucks.