The map cursor is a circle, and you have to tilt the galaxy plane to have it show up (iirc).
I think when I can't see the blue disc it is because the cursor is a lot further away than I thought and I'm zoomed out more than I thought. And when I zoom in and bring the cursor back to me, I often need to then translate up or down to get close enough.
But maybe it could be something as simple as being in "map" mode and having filters set so that you can't see some systems? Maybe check the filters or try "realistic" mode to have all the systems show up.
I think when I can't see the blue disc it is because the cursor is a lot further away than I thought and I'm zoomed out more than I thought. And when I zoom in and bring the cursor back to me, I often need to then translate up or down to get close enough.
But maybe it could be something as simple as being in "map" mode and having filters set so that you can't see some systems? Maybe check the filters or try "realistic" mode to have all the systems show up.