The most common cause of missing parts is shells butted up against each, sharing the same 3D space on two or more faces. NetFabb Basic does everything but combine shells. Shapeways Mesh Medic combines the shells, but can get confused as to which parts should be kept when combining shells resulting in missing sections. Overlapping shells just slightly can help cure the issue, or you may need to create the model as one shell.
NetFabb Cloud Service will boolean seperate shells, in the same way Shapeways does, and is useful for combining shells at any stage of a model's build.