What caused the main problem seemed to be several of the face normals were facing the wrong direction. The normals direction indicates a surface at the starting point of the normal. So for example, you create a cube, flip the normal of 1 face. The cube is still manifold(watertight) but with that normal facing inward, Shapeways regards that faces surface to be inside the cube,not on the outer surface like the other 5, which face outward, so its rejected.
Yea its sorta picky, but makes sense when the model needs to be represented in real terms, not just a subject for a render.
Duplicated vertices can also cause numerous problems.
Just remember to check to see that the normals of a mesh are pointing in the direction that will designate a surface thoughout its design. Especially after any operation on the mesh(boolean, subdivision, mirroring,..,)