Comment 14 for bug 475466

Actually the driver treats BusType option PCI and PCIE the same, then applies PCI or PCIE depending on which generation the card is. However there is some tweaking logic further up which treats PCIE IGP cards as PCI. This should probably have been the case for you. So if the initial detection would be PCIE (and not AGP) it would have ended up as PCI (which worked for you before).

This was changed in July, hence the breakage in Ubuntu 9.10: http://cgit.freedesktop.org/xorg/driver/xf86-video-ati/commit/?id=57f2c83a22f27567506c555af431f89e6031204c