I had a similar problem a while back when trying to print a metric threaded hex nut and bolt. The bolt came out fine but the central hole in the nut got filled in. The solution was to turn off the "fix horrible" features. If your 3D design tool creates proper watertight models then these fix features are not needed. Unfortunately, SketchUp is one of those that often fails to create watertight models, but you can download a plugin (Solid Inspector) that checks your shapes for correctness.
My original discussion here :-
http://umforum.ultimaker.com/index.php?/topic/4548-experiment-with-threads/
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zoev89 73
Is the square water tight? In the cura expert settings you can also play with fix horrible a and b and check if that solves the issue. Looking at the layers in Cura you can see what it will do. If the square can not be found in layer view then it is no use printing it.
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