Good to know you tracked down the cause. I suspected that was one of the possible reasons for what was going on: web pages can be configured so they can't be embedded, and this is usually the underlying issue when Story Map authors aren't able to embed web content in stories. It's not a limitation of Story Maps: web content that is configured to prevent embedding can't be embedded in anything on the web. In your case it sounds like those pages were temporarily changed to be in that mode but have since been fixed to allow themselves to be embedded again.
Rupert