It sounds to me as though your lashings are too loose. If you posted a pic of them, it would help us assess the technique you're using. When I do my own, I run several strands through the beam and gunwale, then wind around the resulting loop to pull it extremely tight. You can see this in some of the photos in my "SOF #3" album at the link below. I have never noticed any gapping or shifting of the gunwales once the beams are lashed in place. While it's true that the skin will hold the boat together, relying on that too heavily could lead to problems down the road.

The material you use for lashing can also make a difference. I only use polyester lashing materials, as they don't stretch and aren't affected by humidity changes. If you're using Nylon, that may be part of the problem.