If you aren't using SJ's slot modder, I know that you have to manually set what the boxes look like on screen in addition to changing what type of box it is.
Slot 16 Xpos := 496
Slot 16 Ypos := 282
Slot 16 Group Name := Shield 2-1
Slot 16 Comp Type Allowed := Shield
Slot 16 Comp Type Abbreviation := S
Slot 16 Comp Box Color Index := 3
Slot 16 Ship Section := Hull
Slot 16 Ship Side Facing := 2
Slot 16 Weapon Firing Point := 0
Maybe Comp Box Color Index needs to be changed, or Comp Type abbreviation.
Possibly, if you have added a totally new box, you just need to change the Number of Slots line near the top of your ship's entry to include your added boxes.
Hope this helps!
