I'm guessing it didn't fill the holes because of the multiple-poly problem with the mesh? That's what I'd assumed anyway. I'd be interested to know if the 'Merge Points' command also merges any associated vertices and polygons. I think there might be a few more of those multiple polys in there- the mesh is looking a little suspicious in places when I try to map it in UVMapper.

Here's the pic Steve sent, to add to his post above.