Hey Neil,
in my opinion, gun ports always seal with the hull, otherwise water can collect in the corners and be pressed into the wood. This would make them leaky and, if there is no sealant there, they would start to rot. Question:
Could it be that you have fitted them the wrong way round? It looks like you've attached them from the outside in the picture. If these gun ports have this width, then they must be planked inwards and either planked with the frames, then they are no longer visible but flush, or you sand them down completely to the planks.
Cheers
Günther