There is the portal object and then the row within the portal. Both can have fill colors specified and the rows can have different colors for the primary, alternate and active states. So when you select a portal while in Layout mode in order to change its fill color settings, you next select either the Portal or Portal: Row in the upper drop down and then, for the portal row, the state for which you want to specify that color. (And portal setup will then control whether different fill colors for active, normal and active states will be visible.)
Thank you! I had not seen the Portal: Row option. My problem has been solved.
I figured this out for myself after some frustration.
I have a question about this though: when I change the portal fill colour, instead of the portal row fill colour, does this setting actually get reflected anywhere on the layout?
If not, it seems odd to be able to change a setting that doesn't actually have any effect.
If it did have an effect on something, then it would be more obvious to a user to think "oh, I changed the wrong setting" instead of "I changed the setting but it didn't work". If FM were to disable the ability to select the fill colour of the portal, that might make it easier for people to realize that they need to change the portal row fill colour instead of the portal colour.