No summary dots for flagged items?

I use the latest universal version of OmniFocus 2, both on my iPad Mini 2 and iPhone 5C.

I remember seeing summary dots for flagged items before, as described in

But now somehow I only see summary dots for my due items, in both project and context view. In other words, these are not coloured dots for flagged items.

I’m sorry, but I’m afraid OmniFocus has never shown orange summary dots for flagged items – and the documentation you link shows an example that contains due soon and overdue items. Perhaps you’re thinking of the yellow due soon dots?