Most of Shapeways rejections come from a manual check just before assembly into the "build".
This check is performed by a human, using Netfabb (or a customized version of it).
The people doing this have seen thousands of prints, and can generally spot trouble areas just by sight.
I understand that there is an automated check done at the time of upload, but the parameters on that check are VERY loose. Mostly it checks to see that the overall boundaries correct, and is any part too thin for some specific material. That's why when you upload certain models, it's ONLY available in WSF or why it's NOT available in Sandstone, etc.
But, the actual (final) geometry checks are done by a human (at this time).
Netfabb itself does not do an automated check. You can use it to manually ckeck things, but if you miss something, the production people might find that one spot you missed. There is a new program out there (referred to in another thread) that seems very interesting to me. It will give you a "heat map" of your model with coloring based upon the thicknesses.
The problem with an automated program is likely going to be that it will fail airplane wings every time they are checked. The humans know that a certain amount of "tapering" is acceptable, but the automated programs to date don't make that decision correctly.
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One thing to understand.. not all models are rejected BEFORE printing. Shapeways actually goes a bit overboard TRYING to make prints work, and they lose a good bit of money on prints that don't survive being taken out of the printer, or they don't survive being cleaned, no matter how careful they are.