I backed up my saves, undid the Deny Write Access fix, loaded into the game, made some quick- and autosaves, and exited a few times.
Nothing is now being written to the Steam\userdata\...\22380\remote folder, and my saves seem to be staying properly.
Now, I also read that they have once again turned off Steam Cloud for this game, so it is possible that that's the real reason that the saves are working. When I first installed the game on Tuesday evening, I had no save problems. I has read about it and tested for it, but all seemed fine. I now know that Steam Cloud was off for troubleshooting at that time. On Wednesday, my save problems started (I assume after they had turned Steam Cloud back on).
Some people are saying that the patch ruined their d3d9.dll fix, but that hasn't been the case for me. I only spent a few minutes in-game this morning to test the saves, but performance seems fine here.
Anyway, the save system seems to be working as intended at the moment, and I haven't seen any new problems. Can anyone else confirm that this is the case for them?