If you had looked at the part in xray view it would have shown errors in red. Any red is where you are looking through an odd number of planes which means there is either a hole in the part or an extra wall such that there is no inside and outside.
You probably could have fixed this with some combination of the 4 "fix horrible" checkboxes in expert settings.
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ilsaarin 2
Answering to myself: STL files were crap. They needed to be fixed. Microsoft service did the job because I haven't learned how to use netfabb yet.
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