Well - for starters, I wouldn't waste time on either 12 or 16, unless you're truly desperate for potions. The RoI from 20 is infinitely better.

That aside, often small changes in speed can result in completely changing the order of your champs, which can very much change your outcome on auto. Same goes for booking. And, ironically, sometimes clearing things faster can actually reduce your chances of winning, since you don't have the right moves available at the right time.

All that said, you say you're trying it on manual and failing. That's surprising. What specifically is causing you to fail? What team are you trying to run? Are you clearing the shield from the boss and/or blocking the buff?

Just for the clarity - there were no changes in any of the levels of Potions dungeons in the recent patches. Please check out the artifacts you use for the Champions. Perhaps you used different copy of the same Champions. Some Champions also might have had some modificators from Faction Guardians first time, but not the second time.