This is turning out to be a problem I'm encountering with some frequency. It seems to be related to something about the mesh that Simplify3D doesn't like, as often times Cura and/or Slic3r will work with the same STL file just fine and – usually – running the STL through the online netfabb mesh repair service solves the problem.
The specific behavior I'm seeing is that S3D will generate – seemingly at random – solid layers where no such surface exists in the model. Usually this results in filament being extruded into thin air, sometimes bridging quite some distance. It creates a diaphragm (as a bridge) where none existed in the model.
I've seen this behavior with models that I've created and exported from Autodesk's 123D Design software, but today I'm seeing it with the stock, unmodified STL for 3dbenchy obtained from thingiverse.com.
I tried to run the 3dbenchy STL through the Netfabb repair service today but couldn't because it seems to be down. Tried using the repair options available in Netfabb free and meshlab to no avail.
Changing the layer height modifies where and whether the phantom diaphram bridges are generated, but eliminating them in this way is a trial-and-error process of guessing random numbers, and is really just obscuring the actual problem.
I've attached my factory file. I'm running Simplify3D 3.0.2
I've found one other report of this issue in the forum here: viewtopic.php?f=9&t=3444, but no true technical explanation of the exact nature of the problem, and no real solution (outside of the Netfabb service) provided.
Here are some screenshots: