I’d say it has something to do with number of images, though it’s hard to say. I know that rescanning 46000+ images is slow and tedious, but as I can not reproduce the issue, this will be hard to solve. I suggest maybe you could try downgrade couple of versions to find where the issue started. Also, it would be beneficial to know whether this also happens when you have only 4000-5000 images in database.
Maybe you should contact me by email, so I can send you previous versions.