Do you know if that issue is reproducible in other systems? The Nehalem generation Chipsets had issues with Interrupt Remapping, so when I see people with these systems having issues when using the IOMMU, I would point my finger there first.
You may want to try disabling Interrupt Remapping for the host with intremap=off as Kernel Parameter in your Boot Loader config file and/or enabling Unsafe Interrupts for VFIO with vfio_iommu_type1.allow_unsafe_interrupts=1. I don't know if that can help you, nor if doing that breaks passthrough itself, but if you have no other leads then its worth a try...
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