I'm currently in the process of completely reworking the mod and hitting the same bug. it seems to be a genuine vanilla api bug.
the problem is really on what the api returns on
local entities = search_area.surface.find_entities_filtered{area=search_area.bounds, limit=result_limit, type="entity-ghost", force=search_area.force}
interesting: placing a new roboport next to the old one, removing the old one, placing a new on on the same pos -> changes nothing.
removing the roboport in question and having the ghosts out of reach of any other roboport, then replacing it -> fixes the signals (at least from what I tried)
here is a tiny test map with the same bug: https://www.dropbox.com/s/0fjdo5iw9kms9wu/ghost%20scanner%20test%20-%20BUG.zip?dl=0
update: my time usage is terrible xD, just as bad as the original mod but a lot more consistent.