It's by your Achievements. Your actual levels do not affect your ranking, except that every 5 levels you get an achievement.
When sorting by individual classes it's looking for levels, and then it will show whoever has the highest level, followed by achievements via lodestone.
The problem with ffxivpro.com is that sometimes achievements only update once a week. While clicking Update manually will update your classes, often it does not affect your ranking because it rarely downloads your achievements (notice they always seem to be like 4 days behind your lodestone) so you will often fall 20 ranks or so, but once your achievements update you jump ahead 80 or more.
Edited, Jan 24th 2011 9:46am by Eadieni
This is not true.
My overall points and ranking changes everytime, even if I only ranked up 1 Rank in any class(no matter if its a 5-step Rank with Achievement, or anything in between)
And no, my achievements never did anything for my ranking on FFXIVPro. It was always Ranks only. And I'm also at the same place on "Class specific" rankings since I hit 50, never changed.
PS: You can only drop 20+ Ranks and rise 80+ Ranks if you're pretty far behind on your server, or else you will never see that big of changes in your ranking. I'm jumping back and forth between 5-10 ranks max atm. Edited, Jan 24th 2011 11:21pm by Shezard