Generally the X server driving the AGP card has to be started first.
This can be acomplished by manually starting X or using gdm as desktop manager. You'll have to abstain from using xdm or kdm, as they start the X servers at the same time.
AGP sever restart leads to system crashes. In gdm.conf, set AlwaysRestartServer=false.
The XFree-4.3-prefbusid patch/binary fixes most of the problems. In case the X servers are started in the right order there are no lock ups.
Nvidia TNT2(AGP) + Matrox Mystique(PCI)
Nvidia TNT2(AGP) + S3 VIRGE/DX(PCI)
Nvidia GeForce4MX440(AGP) + TNT2M64(PCI) + TNT2M64(PCI)
Matrox MGAG400(AGP) + Matrox MGA1064SG[Mystique]PCI
Matrox MGAG450DH(AGP) + ATI Mach 64(PCI)
Matrox MGAG550DH(AGP) + Riva TNT2-M64(PCI)
Matrox MGAG550DH(AGP) + Geforce4 420(PCI)