I didn't open up your model, but looking athe isometric view, I would suggest that "less is more" when it comes to surfacing. You are usually better off when you have the least possible number of profiles and the least possible number of points in your splines. You might also find that it is better to split your hull into two or more surfaces, say one at the front, where it changes fairly quickly, and one at the back, where it changes much more slowly. Boundary Surfaces give you more control than Lofts.
Niall, your hull surface is rippling and buckling for a couple of reasons.
First what Jerry said: you've got too many cross sections and minor irregularities from eye-ball tracing the sections and a general lack of control over the spline weighting is producing surfaces with a lot of inflection points where the curvature changes from concave to convex. My suggestion is that you start with two sections and try to tweak your guide-curves by dragging the tangency handles and by adding curvature pionts (not spline points) to make guides that match your nautical lines.
Second, you want to use boundary surfaces between the bulkheads and fill surfaces at the ends. Boundary surfaces and lofts that have to collapse to points, develop singularities and produce unexpected results when thickened. When you're building your fill surfaces, use the edges of your boundary surfaces as tangent curves and then you can set them curve continuous.
Third: if you're hull is symetric about a plane, only model half of it and then mirror it. This requires that you set up tangent controls for your profiles at the plane of symmetry and that you have a guide curve on it.
Boundary surface does very poorly with many sections. Try to use two edges and a guide curve or two and two sections. Use curvature display and zebra stripes to find imperfections. It is best to think of all surfaces at having four edges. Singular points cause trouble. Beware of projecting two planar curves that share a point. The resulting curve will not go all of the way to the point. A fine old bug from 2003.
I am designing airplane fuselage shapes. I get excellent surfaces using the GW3D add in from cadcamcomponents.com. They have an excellent controllable conic surface that will give you a beautiful fair shape. There is also a geodesic mapping feature that will generate a flat pattern with minimum distortion. This is good for cutting a core material for composite construction.
When you look closely, almost all Solidworks surfaces have defects; butt cracks, hogbacks, ripples, curls, tits, wrinkles and gaps. These cause trouble down the line when surfaces are thickened or manipulated.