I've experienced the same problem intermittently throughout various system rebuilds (I'm restless, what can I say?). On one system, the stuttering seemed to have been caused by specific versions of the ATI drivers, but I forget which of my three options (packaged, Windows Update drivers or downloaded from ATI's website) would fix the problem.

I've moved to a notebook, though, and after wiping the system and reinstalling Windows on it, the same "hiccup" problem showed itself where it wasn't before, and juggling drivers isn't doing the trick this time.

The really frustrating thing, in my opinion, is that it also happens on the title screen (which shouldn't be affected by bandwidth or latency issues). However, the performance of the old Vana'diel Benchmark 3 is unaffected, no hiccups, so that can't be used as a litmus test.

This is why I hate Windows gaming. But the alternatives are a three-second freeze every time I change areas on Xbox 360, or black screens when the PS2 tries to load cutscenes (e.g. chocobo raising), so... I dunno.

I'm about to try FFXI under WINE.