Two thoughts:
1. Only systems close to your gal map selected position show up. So if you are looking for stars on the other side of the galaxy, you must move your selected position close to that area. Same concept if you are looking for black holes etc.... you must move your selected position around to see the systems within proximity. And of course if you zoom out too far from your selected position you don't see any systems.
2. As mentioned above, if you reinstalled the game the gal map might not display visited systems using the filter. However, if you manually select a system that you have visited it will show you the icon on the right to see the system map. Tedious, but it is a method to confirm if you have been there.