This is interesting to me; I’ve found that JPEG images that have been rotated (in Shotwell) before PhotoStructure saw them haven’t been rotated in PhotoStructure. I just assumed that Shotwell wasn’t storing the information in a place where PS would pick it up, but it seems that’s unlikely from your reply @mrm.
Mentioning it in case it’s related. I’m not in need of a fix as I’m going to move to darktable and am unlikely to continue using Shotwell…