I don't have Dish, mush less a Dish DVR, but the symptoms sound like either the harddrive or it's drive contoller going bad. If the DVR has the ability to let the user format (of course losing any stored programming in the format process), you may want to try that, if you did not already.
Of course, this does not preclude the possibility of it being a software, RAM/ROM/BIOS or other component issue.