After fixing my non-manifold errors on my mesh, I ended up getting a windingcheck error that I have no idea how to fix. Has anybody seen this before? -Chris
Never saw that before.. but just a wild guess, probably something to do with normals. (normals can be defined be the vertex/edge order on a polygon, counterclockwise or clockwise determines normal direction) You could try a "fix normals" or "unify normals" filter/modifier in meshlab.
If you guys are still interested, I did end up fixing this error... ...it's hard to describe, I don't think it had anything to do with normals, but the way the vertices were connected by edges was kind of "messy" (the faces were auto-generated). I re-autogenerated the faces with a different tool and they came out much cleaner. If anyone is getting this problem persistently, perhaps I can give more details.
I had the Windingcheck error too. Turns out Shapeways defines "inside" as where the normal is pointing. I had all the normals pointing outside. All I had to do was flip all normals and it was fine. I was using Blender.