Do you have to go to a new galaxy? I had it perfect where the atlas mission just said explore, but then i made a dumb decision at the last anomaly that set me back on the path with the annoying pop up. Now the anomaly is not showing up so I can change it to black hole. So I’m thinking of beating it to get rid of the notification.
Had this happen as well. They should show in the same system as your base. It did take some time and I did jump around to other systems, but finally they showed.
Anomalies should show up as you jump around. They dont seem to appear in system I previously visited, but they do appear each maybe 8-10 jumps.
The Anomaly has a few different triggers though sometimes some of those triggers decide not to work temporarily.
They will appear after,
X amount of Jumps
X amount of time has passed since your last jump,
or after loading a save, when you go into atmos (without leaving the system you loaded into) they will arrive (sometimes as soon as take off)