I know I've seen my TivoHD (and possibly S2DT) with both tuners on the same channel on more than one occasion.
In fact, I just turned on my TV, and sure enough, my TivoHD has both tuners on the Discovery channel. I don't know if there was a reboot last night - is there a way to check?
Strangely enough, the last thing I recorded (programmed by me) on Discovery was at 1am this morning. Yet when I looked at the suggestions that have been recorded, there have been recordings on 5 different channels starting at 1am, none of them being Discovery. None were overlapping, so the suggestions could have all been on the same tuner (call it T2), but one suggestion did overlap my programmed recording.
This is unrelated to the OP, but interesting anyway.
 I don't understand the OP either. What are the expectations vs the exhibited behavior?