Hi, Bob
I was tested your model with 2013 and cannot reproduce the problem. I have imported the test.sdy from your zip file, changed the sequence to fill-pack-warp with all the default parameters and run the simulatiuon. After this I have rotated the whole model by 90 degrees over X axis and run the analysis for the new model. The models and studies are attached.
Comparing the results by the "compare study" tool gives only three differences: Names of the result files, Projected Area and Maximal Clamp Tonnage.

I thought that maybe the difference in pressure is too subtel for the Compare Study tool to pick but the log files themselves (see atttached screenshot) show no differences.

The only difference I could notice was a subtle difference in deflections:

while the maximal deflection is the same: 0.2569 mm, the minimal deflection is 0.1080 for the original model and 0.1074 mm for the rotated model. As Yannick said this subtle difference is probably to postprocessing of the best fit. Do not worry about it.
I an thinking that a small difference in the peak pressure you have obtained might be due to a slightly different matching. Before doing the analysis of a dual domain model the software have to do some geometrical processing - determine thickneses and matching elements. Every release Autodesk Moldflow makes some improvements into this process. Matching takes some time, so the solver is trying to save the info in the study file once it done and redo the matching only if the model is changed. If a model was first matched by an older version of an AMI and then rotated then the new model would be matched by the new version of the software. Also in the past the matching by GUI (done to play some diagnostic plots or during importing of CAD models) might be slightly different from matching done by the flow solver - I believe it is fixed now. The difference in matching might account for a very subtle difference that I would not worry about.