HoMM3 HD is a mod (add-on) for the game Heroes of Might and Magic 3.

I don't have this flickering issue – there's not even a hint of it; everything looks clean. I'm playing in 16-bit mode. I tried to trigger it in other modes, but it didn't work. :)
And the four windows in the artifact merchant have always been there. Maybe Baratorch isn't even aware of it or doesn't consider it important. And it doesn't seem to affect anything; it just looks a bit off.