I'd been experiencing some very, very faint lag for some time now. It wasn't really noticeable unless I was staring at my character; it was a microsecond freeze once a second, almost like the old HID device bug but nowhere near as bad.
It's been bothering me since it started, like an itch I couldn't quite scratch.
A bit of research led me to an FFXIAH thread about similar issues, and the culprit has been pinned down to Oracle's Virtual Box.
As soon as I uninstalled VB and BOINC, tada, the lag stopped completely and FFXI is running at 29.4 FPS, steady as she goes. (BOINC is the application that used VB; without VB there was no point in having BOINC. It's used to run science experiments, in my case the Test4Theory LHC@Home program.)
So if you have unexplained micro freezing in FFXI or any other game and you're got Virtual Box installed, you can try installing it to see if it improves performance.