Loosing geometry after running snappyhexmesh for the ship
 

I am working with the DTMB geometry with a length of 5.72m (Lpp). When I execute snappyhexmesh I am loosing geometry as can be seen from attached figure. When I performed interfoam there is water inside the ship. I am attaching how my geometry look after executing snappyhexmesh (surface refinement level (0,0)).
I am also attaching another geometry of length of 2.5 m (Lpp). On this ship when snappy with a surface refinement of level (5,6) was performed, no loose of geometry was observed.
The ship I mentioned in the first was taken from http://www.simman2008.dk/5415/5415_geometry.htm , the size of stl file is 1 Mb, but the ship I mentioned second (L=2.5m) has a size of 20 Mb.
How I can rectify this issue. Is that because of lacking cad geometry repair, if so what repair work I should do for my ship.
Any suggestion is welcomed and highly appreciated
Waiting for a fast reply from someone
Thanks and regards