Hi again del-pepite,
I thought this was a good summation of what QE is:
http://kb.iu.edu/data/ajeb.html
Your AGP card is QE compatible. Your PCI card is not. No PCI card is, as far as I know.
I went through this topic once before myself. It's easy to add a PCI card to your Mac but it seems *any PCI card* will disable or interfere with using Quartz Extreme. So that's a lot of modern Apple software.
I tried to get this solved talking to Apple. But they were completely unconcerned. They just said they didn't take into consideration older models when creating new software. At least in this case.
Actually I was pretty angry as I had just a month or so prior bought the PCI card that The Hatter mentions above. Still on the market and advertised. However neither Apple nor ATI is really making public the fact that using PCI cards disable some software when installed in Macs. If one has a PCI card and has just bought iLife 08, they will find that iMovie 7 doesn't work, at all. That's one of the four apps in iLife 08. Or a quarter of the price.
I don't know how you would manage a 3rd monitor without the card interfering with QE apps. Or what you could use in lieu of a PCI card. Only way I can think of is to have an s-video output on your AGP card. That could go to a tv but another monitor, I don't know.
Write here to try to make a difference, I think the ball is in Apples court:
http://www.apple.com/feedback/macosx.html