Yes, I know. I'd been using focus following and auto-raise since 1986, and set every X display I used to do it and was able to all through the later Linux years. Even set it on Windows machines and then when discovering that every tweak that allows it on Windows was such a crappy implementation I'd set it back to default.
Until I got a Mac. At that point all of the other aspects of Mac OS X were discovered to be so great that I just decided I'd live with click-focus and no auto raise. In this case the Leopard (heh) changed it's spots.
Heck, on a number of occasions auto-raise got me into trouble when I'd enter commands in one window and somehow I moved my mouse and it would raise the window behind it and I didn't see it. So I'd enter the command in the wrong window. Like deleting a file now in a different window where I'm positioned over a very important directory or file. Or I'd be talking to someone over a chat window and instead of doing what I wanted I'd end up typing tar cf - * | (cd /foo/bar; tar xpfB -) to my wife in the chat window. Especially bad when I knew that would take awhile so right after hitting return I'd get up to leave without looking at the screen and not only was my copy not going to work, but my wife would be all 'huh? *** was that?' in the chat window.
Anyway, my advice would be just to let go of the auto raise. Besides Exposé is vastly superior for switching windows than auto raise. I've got it so I set my fourth button to activate with the fourth button on my Mighty Mouse which is a squeeze. I squeeze, move to the window I want to go to, and squeeze again. It select the window, puts the focus, and raises it in just two quick squeezes. You can do that with any multi button mouse you can assign Exposé-all windows and once you get used to it it's way quicker and more intuitive than follow-focus/auto raise ever was. I truly, truly miss it when I have to work on my employer supplied Windows dell, much more than I would miss auto-raise, and wouldn't hack it into XP even if I still could (which I probably can, but I just live with click-to-focus or the taskbar.)