This is happening even after commit a0695cb (which I thought would fix it).
Looking through my savegames, it seems the most recent one with a correct thumbnail is from 2aee68d, which is about a month old. Might take pretty long to bisect this.
Edit: It seems that thumbnails are generated correctly on software renderers. Also, the screen resolution / scaling changes the size of the little square area (the lower the resolution, the bigger the square is).