Here are the screencaps for my settings:
Nothing special, I used the vertical medium theme and haven't touched the CSS. I also didn't use the automatically embed beneath posts option, because it put it into a weird spot in my articles (as there is a lot of stuff below the content), so I used the custom shortcode:
Which was working beautifully, and it automatically grabbed posts from my site. By choosing posts manually, I did mean clicking the orange button and going in to choose related posts manually, and adding them to the article. That doesn't seem to be working now either.
I don't really use that many plugins aside from cross posting plugins for FB/Twitter/etc, and a few layout changing plugins, but those are only for the desktop mode. Again thank you so much for looking into this.