Would you be able to test this with upstream qemu?

git clone git://git.qemu.org/qemu.git
cd qemu
./configure --target-list=x86_64-softmmu
make -j4
cd x86_64-softmmu
./qemu-system-x86_64 -enable-kvm -m 512 -device pci-assign,host=03:00.1 -boot d

If that works, then we just need to look for the commit which fixed it.
If not, then either there is an existing bug upstream, or some bios
setting is likely not right on your system.

** Changed in: qemu-kvm (Ubuntu)
       Status: New => Incomplete

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https://bugs.launchpad.net/bugs/1181777

Title:
  kvm: freeze a guest with a NIC PCI passthrough

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