I think linux thing is a case of "real programmers code and test under linux, then cross-compile", which results in a code that is far more tailored to linux systems.
Intel processors (especially lower-end ones) tend to have a smaller L2 cache and if I read the scrypt paper right, that somewhat hobbles them.
See comparison here http://www.hardwaresecrets.com/article/819
Apparently, Core i5-750 specifically has whole 256k of L2 cache less, while scrypt as implemented in Tenebrix eats up no less than 128k of cache. This not only "keeps intel down" but will (obviously) reduce the potential benefits of HT.
Now, obviously good compile flags might mitigate that a bit, but you can't make the CPU grow some more cache, so some AMD superiority is to stay.
As for windows/linux programming, I am not a programmer (just an overclocking enthusiast) so I can't give much useful info on that
P.S. (to some comments above)
You know, I am starting to get mildly annoyed at the "Scrypt-PoWs are friendly to custom hardware" myth.
No they are not.
Even in their meekest weakest incarnation, they render CPUs the most likely winners in bang-per-buck competition, simply because CPUs crunch them decently with bearable power consumption and, due to economies of scale are cheap.
Custom hardware would need to compete with something vastly cheaper and vastly more available.
A Rational Well-Funded Attacker won't deploy thousands of exotic computation devices $5000-10 000 a pop. He will use his huge money supply to build a huge cluster using COTS CPUs.
Having said that, idea of defending against a Well-Funded attacker via technological tweaks is a fallacy - like I already said elsewhere, it does not matter whether your algo is CPU friendly, GPU friendly, or Babbage engine friendly.
Attacker will just buy a bigger pile of "most efficient hardware" than you could afford.
That's the benefits of being well-funded.