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So just my luck, I originally printed yours and at least 5 different variances of this including the dual filament one, and every single time it did the same thing. I had restarted Simplify3D at least 2 times, I compared to cura which didn't have the problem. In S3D, it was closing off the internal chambers by about 4-5 layers. I'm not talking about a gap slightly closing, they were sealed. So in response I started goofing with shell settings, layer height, a few other minor tweaks and after no real difference I gave up. I then reloaded my original settings by clicking a different printer profile and back to mine and answering "No" to updating the profile, then magically the emulator was drawing it correctly. Really frustrating because I would have loved to actually find the setting that was causing the issue. I'll keep playing with the settings to see if I can reproduce the error.