Need Help with highlights

I have a game in re-design mode. The situation is this: I’m using Vassal 3.2.16 on a Windows 10 laptop.
Main Map has multiple boards that can be flipped, each board has multi-zone grid, main zone has a numbered hex grid. Every city on the hex grid is in turn it’s own zone (so that it reports the city name when entered). There are ‘city’ counters that are transparent and in ‘at start’ stacks of one per city. They have traits that show up on the board when the city is bombed, changes control, etc. (or at least that is the idea). The game also has a nuclear component represented by missile counters that when delivered to a target invoke an ‘area of effect’. The issue I’m presently having is that areas of effect for city control and nuclear blast radius do not show if the target is in fact the city zone or city piece. Also, when the board is flipped the ‘at start stacks’ are no longer in their respective cities.