If you check the help text that appears when you mouse over the number of systems, it states that doesn't apply to Known Stars games.
I think I’ve requested this before, but would it be worth thinking about the design of the New Game screen some? It could use a few improvements.
For example, the Known Stars option is a big choice that really defines how the rest of the game feels. When enabled, it causes several other options to be ignored. Perhaps this should be a big hint that should inform the design of the screen. Imagine having radio buttons to select between Random Stars and Known Stars. When Random Stars is selected, the options that only apply to Random Stars game are enabled and those for Known Stars are disabled, and visa versa. For easier comprehension, these options should be visually arranged so that the association is obvious at a glance. Or see the attached picture. Of course it is a GTK Assistant window rather than a Windows Wizard window, so it looks different.