This didn't happen on my first playthrough this year, but now that I've restarted the game, it happens every time.

I finished the Forgotten Shrine of Neferti, the Obelisk, and the upper level of the Ruined Temple of Harvest, but when I went to the Temple of Set, it was laid out as though I had already completed it: all monsters killed, all treasures taken, all doors open, even though I had not been there at all in that playthrough. Then, I checked all my save files and ALL of them were corrupted, so the same thing happened in all of them. I uninstalled and restarted the game, but after a few launches, the bug recurred every single time and ALWAYS corrupted all my save files as well. Has anyone EVER had this problem? (I haven't checked any other sections of the game other than those mentioned above, so I don't know if it corrupted other dungeons, but I wouldn't be surprised.)

One other thing. I was using Gotcha download of the corrected Code.2 which I used to correct the freeze during the ending video. It solved that problem, but I'm wondering if it introduced this bug. Does anyone have any idea?

The only thing I can say is that I've not seen this happen during my last play-through, but that said, I might not have been using the updated code.2 until later in the game.

I always do the Temple of Set before going to the Temple of Harvest; am wondering if picking a different order messes things up?

No. Now that I have run the game again WITHOUT the Code.2 upgrade, I feel I can say with confidence that the bug at the Temple of Set was caused by Code.2. I have had ZERO problems with the Temple on this run through, and that's after checking it about 20 times. My order of play has been Forgotten Shrine of Neferti, the Obelisk, and then the Temple Grounds portion of the Ruined Temple of Harvest. I have checked the Temple of Set, as mentioned above, about twenty times throughout and there was no problem at all.

I am afraid your Code.2 download is somehow corrupted.

Damn. I hope the guy who created this patch will come across this. (I didn't make it myself.)
Thank you for the feedback. I'll make a warning in this thread:
https://www.gog.com/forum/dungeons_dragons_ravenloft_series/this_is_why_videos_do_not_play_and_the_game_crashes_at_the_end