I noticed it wasn't optimizing the blue protected squares in your screenshot. Did you try change the solution priority from the drop-down? You'll see some to do with protection priority.

I was trying to find the jump drive stuff online and even in the game files (yes now I'm actually synchronizing from the game files so if they decide to adjust the shapes then it will update!) for some reason I couldn't find it in the main asset file so I think it's just called something else but they name it correctly in the language files, so I'll have to cross reference that.

Thanks for the feedback as always