Oldcargirl,
I don't know why a manual (not instigated from the Guide) auto-tune timer scheduled for say 3.30am would begin no longer waking up your box, after 2 weeks, but if you are certain that's the case, fair enough.
Do you have any other actual intended timer recordings set to fire or in progress around about 3am? If you have, these could push-out the nightly update ocurring to a later time, I think, and then your auto-tune one would have happened too early to be after the nightly update.
Perhaps you could get a universal remote which has a built-in timer, and you could program it to send the Dish box a 'Select' (not Power) command say every 30 minutes between 3 and 6am ?
It's a bit of a clunky solution, but it might possibly fix your situation. Best of luck ;-)
