Multiple shells are not necessarily something to be worried about. If they are intersecting, the slicer will view them as one (think vacuforming, only the outside edges matter). However, if they are merely adjacent, that is when you might have issues.
In Maya, I can 'snap' one shell to be exactly aligned with another so that no matter how far I zoom in, they are always touching. Alternatively, if I free-hand position two shells next to each other, sometimes you'll zoom in and find there is still a super tiny gap. This is when you'll have issues as the slicer thinks there should be space between them.
Holes are more problematic. John mentioned in another thread about handling files in different programs. Netfabb may identify a hole, yet still call the model 'water tight', however the Photon Slicer may recognize that hole and think otherwise.
Yet a third issue to be aware of, and one I think might be affecting Chris's model, is face normals. Think of these as clothing. With the exception of reversible ties and such, clothing has an inside and an outside. If I put on a sock inside out, that's not blatantly obvious to the outside world, but our 3D programs sure know it. Going back to the vacuform simile, as it begins forming over your foot, suddenly it thinks the inside is outside, and we start getting conflicting results, or random triangles. (Netfabb being more sophisticated, might be recognizing this and auto compensating, therefore able to call the model water tight.)
I'm not sure how to solve that in Netfabb or Sketchup, if it is an issue at all. But like Jason, I'm happy to take a look at the model if you're willing to send a copy.
