vps_dxb,
My speculation is partly based on having looked into arc/GIS a few months ago.- which has some similarities: that there are two factors at work, first that a highly complex, high polygon, large dataset 3D mesh generating program is CPU compute intense, and these components- the Steps 1 and 2 in the program appear highly single-threaded.
The software maker states that the progtram is highly parallelized, but also say that a high clock speed is also desirable. So, in the first instance, the clock speed is going to dominate over core-count. However following the portions that are CPU-intensive, the visualization, is GPU accelerated.
In combination, my thought is that fewer, faster CPU cores, in combination with a high GPU compute might be the solution- hence the idea of even very fast 4-cores in stead of moderate paced 8 cores, coupled with a lot of memory- which you have, and then a Quadro /Tesla Maximus to generate the visualizations.
The other asepct, the notice regarding problems with the two particular Xeon E5-2600 v3 is a bit crytic. I don't think I've ever seen an indication from a software man'f that a series of processors encounter trouble since they are developed at staggering expense with the idea of of extremely high backwards and forward compatibility. So, yes, as you suggest, they may well have missed whatever happened between Xeon E5-2600 v2 and v3,..
The combination of factors is a worry as the E5-v3 notice suggests a situation that has hidden causes and characteristics. It sounds as though you've researched the situation and the unconventional nature suggest not jumping into expensive experiments without knowing more. In the end, you have a highly competent GPU in the Quadro K5200 and in my view this tends to point more towards the CPU single-thread performance. But, then there's the odd "our software doesn't like some E5-v3's" situation clouding the problem.
One other aspect to consider is that processing speed is a relative perception. Do you have a way to confirm that your running time is longer than expectations?
Also, have you ever run a benchmark tests on your system? If not, I can highly recommend Passmark Performance Test which breaks the test into the component subsystems: CPU, 2D, 3D, memory, and disk and using a weighted algorithm, creates a system rating. It's very revealing of weak points in a system. I had below average results for the CPU's on a z620- 19675- and worked out that I should be using registered RAM and the new CPU result is 22645. There's a free 30 day trial also.
Cheers,
BambiBoom