• If you switch your Preview Viewing Method to something you can see, like cross view, and make sure it’s correct, then switch back to anaglyph it will keep the sides as they should be. Does that help?

    So, once loading both pictures, and having (for example) the preview method as Crossview, then adjust the pictures to show crossview, then you can save all the anaglyphs with all sides in the right spot? 

  • Also it isn’t exactly written down but it loads the first one as the left side if you’re loading two pictures at once. You could also load each side one at a time.