Está funcionando agora. Tive que mudar para usar o OVMF bios e o chipset q35.
qemu-system-x86_64 \
-smp sockets=1,cores=4,threads=1 \
-M q35 \
-bios /usr/share/qemu/bios.bin \
-enable-kvm \
-cpu host,kvm=off \
-m 16000 \
-vga none \
-device vfio-pci,host=03:00.0,multifunction=on \
-device vfio-pci,host=03:00.1 \
-hda windows.qcow2 \