While I'm not one of the engineers at Dish, I can't help but think this little loop/bug is partially intentional. The box will ignore the padding to conserve tuners if sequential shows are being recorded on the same channel. Its not quite as simple as you would think to just copy/paste the overlap time between 2 videos. Each recording is stored as a single file. Think of it as trying to add lyrics to the beginning/end of a mp3 file that you already have saved.
PTAT is stored a little different. Think more like a DVD with chapters. The pause timer bar only shows the timer for that chapter, hence why it automatically rolls into the next show.
As for over throwing the "conserve tuners" rule inside the receiver, I have not seen any way of doing that so far. I do know a lot of channels like AMC will recycle a 3-ish hour block especially on new episode nights. During the Walking Dead season I had multiple conflicts, but the hopper would catch the second run of the new episode as it still had a new episode tag (I assume it looks at original air date vs current date for this).
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