Yes, it's only on Zikurat and only in Fortress mode. It's either a bug or the code for spawning that particular flag is simply missing. Hence a simple oversight that can happen to anyone. Especially considering how long it took for anyone of us to notice.
You are 100% right. I never play Pantheon and thus i didnt know about it.
But i just tested it in Singleplayer in all maps in Fortess mode.
So: Zikurat + Fortess = missing valor flag for Dark. Damn! it is so easy to spot. How did we all miss this? It is so obvious.
No wonder the devs missed this bug. Kudos for Spooky