Device vfio-pci could not be initialized when passing through Intel 82599

Issue

When assigning a PCIe device to a VM with KVM and vfio-pci, some PCIe devices will cause the following error message:

Error starting domain: internal error: early end of file from monitor: possible problem:
2014-06-26T05:58:47.482875Z qemu-system-x86_64: -device vfio-pci,host=07:00.0,id=hostdev0,bus=pci.0,addr=0x8: vfio: error, group 13 is not viable, please ensure all devices within the iommu_group are bound to their vfio bus driver.
2014-06-26T05:58:47.483075Z qemu-system-x86_64: -device vfio-pci,host=07:00.0,id=hostdev0,bus=pci.0,addr=0x8: vfio: failed to get group 13
2014-06-26T05:58:47.483102Z qemu-system-x86_64: -device vfio-pci,host=07:00.0,id=hostdev0,bus=pci.0,addr=0x8: Device initialization failed.
2014-06-26T05:58:47.483128Z qemu-system-x86_64: -device vfio-pci,host=07:00.0,id=hostdev0,bus=pci.0,addr=0x8: Device 'vfio-pci' could not be initialized