MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I'm glad you like it.
Your screen shoot is a bit strange.
When i slice the model, at layer 107 the top rectangles already printed.
I think that your screenshot show the top part of the internal support for the upper link.
Layer 93 is an empty layer above the support (it allow easy removal of the support).
Layer 94 is the first layer of the top link. Yes, it prints in "mid air", but I don't see any reason for the lines in your screenshot :/