So are current Pathfinder modules / adventure paths being run with the Pathfinder RPG rules? Or is it still 3.5?
The adventure paths still run with 3.5, because Pathfinder RPG is still in Beta phase and subject to change. The final rulebook will be available August 2009 (just right for Gen Con), and after that, the Adventure Paths will be written for Pathfinder - coincidentally, a new one will start in the same month, so it all works out fine (they wouldn't switch rulesets while an AP was running)