There seems to be some filtering out of small objects based on their volume on upload to shapeways.
(At least for STL which I use)
Here is a test I did reducing a 1mm cube to 0.7, 0.49 and 0.34 sides
Then repeat but leaving the vertical as 1mm
Then added a cylinder and repeated the process.
16 objects should appear.
The smallest cube and the smallest 3 cylinders were removed during the upload (which gives me an approximate idea of what the volume used to filter out it.
The problem is that all of the 16 objects are valid for printing with FUD, no dimension is less than 0.35mm
You can only get around this by combining manifold objects to increase the volume - someting to be aware of.
I may be able to write a small script for my modelling tool to identify these objects but others may hit this problem too.
Paul