Strangely enough, this problem had been happening with my MacBook as well, even with the option activated under sys. preferences.
Even more stranger still, the problem silently fixed itself.
Was it 10.7.2? Perhaps.
I determined that this was just happening in Safari for me, so I disabled the last extension that I installed, which was fairly recent and since this issue started happening fairly recently, I thought there might be a connection between the two. As soon as I uninstalled that extension (RSS Menu), pinch-to-zoom started working again. I didn't even need to restart the browser. Now that isn't to say there is a problem with the Safari extension, RSS Menu, because I reinstalled it and pinch-to-zoom is still working, so try uninstalling some extensions that you've installed lately. If you haven't installed any lately, try turning them off all together, if they're already turned on.