If I understand correctly, some flags on Stack Overflow are hidden from moderators for whatever reason. This behavior needs to be tweaked. This is what is happening now (tested with latest versions of Chrome and Firefox on Windows):
The banner on the bottom tells me there's a flag on the question, but I can't see it without opening its flag history. I don't know what purpose this serves.
The ones above are also absent from our moderator flag queue. But the worst ones close question flags that do show up on the mod queue. When I navigate away from the dashboard, I see nothing at all (no banner). I have to either go back to the dashboard or open the flag history:
This makes no sense. We should be able to see these flags like we see all other flags, on that little banner.