Hi Itchy,
This morning I set up a model as you described. This was a vertical segment comprised of a cylinder - cone - cylinder. A nozzle at 90 deg was located on the top and bottom cylinders. Both the 2D and 3D graphics seem to render the model correctly.
You could submit your model directly to us for further evaluation. Then perhaps we can sort this problem out for you.
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Scott MayeuxCADWorx & Analysis Solutions
Intergraph Process, Power, & Marine