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I was able pin down these two behaviors depending on the length of the path the custom-r folder is located.
In my particular case, running at /home/skrynski/rirAAA1234567/external/custom-r and shorter paths, benchmark exhibits behavior 2.
Past that size, for example /home/skrynski/rirAAA12345678/external/custom-r, it shows behavior 1.
I could reproduce this on prl5 and on my linux box, but not always on the benchmarking machine (where it seems to vary a bit more).