Are you sure? I haven't used the new Google photos, but Google+ photos confused me for a while because it defaulted to displaying "highlights" instead of all photos, where they picked the best one or two out of any similar pictures in the same timeframe and hid the rest. My photos were all there, i just had to use the all photos view.
Yes, I went through all of the settings, and it was weird because I set up backup all pictures from the very beginning. One thing, that is also happening on Android, after an upgrade the app loses some or all the settings.
