Thanks for the response Arnan! I double-checked to make sure the groups are in the right categories. And the shortcodes should make no difference – they are only in the advert settings themselves.
I’ve created a group for every category of post. When I add in an advert, I assign it to only one of those groups. I inject the ads after the 8th paragraph.
We use caching through WPEngine, but purging them didn’t make a difference.