This guy also could have at least linked to a repo of his code... though none of that fancy github stuff was around, Sourceforge and CVSweb was around back then. Without the source we can't really accurately judge, well, much of anything. Compiler flags, JVM tunes (was it warm?), source code, data sets, or hell, even mention of compilers.
Edit: Though his point held hm, not quite 'true' categorically, but you could argue the point. Around '06, Fortran was still largely used, at least bioinformatics (sequencing, attempts at heuristic folding .. stuff), weather prediction, and was a perfect fit for linear algebra.[1] It was accessible and fast enough to be used by post-docs who didn't write software for a living, so presumably the ecosystem was founded then continued to develop within Fortran. Even if it was possible to outperform your simulations in C++ (I'm sure you could get at least fairly close), all of the work you were building off of (e.g. with your colleagues, advisors, etc) were Fortran-based.
[1] This is all hearsay from my father's / his doctoral students work from the late '90s/early '00s when I was in high-school, so I can't really offer sources on hand, but if someone really wants me to, I can fire off an email to him to gather specifics.