This can be due to a couple of reasons:
- The decks in which changes aren't being saved are modded decks. This is a known issue as deck configurations must be saved to the player's profile, but the profile can only store a finite number of deck configurations (just enough deck slots for all the official decks).
- Your profile is read only for the current user in windows. If the game can't write to the profile then no deck configurations will be saved regardless of whether the deck is official or a mod deck.
The most common reason that people complain about this is #1. There is no fix and there is no way to control which decks are saved to the profile. So until WotC and/or Stainless update it to allow for any number of deck configurations to be saved this will be a problem.