It surely doesn't have anything to do with the anti pop-up, because that is a setting that it's internal to the Addon Manager so, it's not really possible the Super Traffic Board can have any effect on it.
Also, if what disappears are the main buildings, they are not handled by the anti pop-up setting, because buildings already have a range equal to the whole scenery area: the Anti Pop-up is only meaningful for smaller objects that by default have less visual range, which usually is ground clutter details like baggage carts, boxes, static vehicles or vertical taxisigns, etc.
What might happen, instead, could be that Super Traffic Board is sending so many commands to the Simconnect system, that is clobbering it. This is just a guess based on your description that the scenery works fine, until you enable the Traffic Board.
If this is the case, I'm afraid there's nothing we can fix from our own side.
