The Nehalem era X58, 5500 and 5520 Chipsets had a notoriously broken Interrupt Remapping implementation: https://support.citrix.com/article/CTX136517 (Love that symptoms list) https://www.netiq.com/support/kb/doc.php?id=7014344 https://serverfault.com/questions/745593/does-disabling-vt-d-and-interrupt-remapping-break-msi-x
Interrupt Remapping was directly related to some x2APIC, MSI-X (Not sure if MSI) and IOMMU features which obviously on X58 platforms don't work as intended. You can try to force disabling them with Kernel Parameters (intremap=off and something else to force old xAPIC) and see if it improves. Google around also the X2APIC Disable Bit in the ACPI DMAR Table (I recall that I wrote something related to it). VFIO had also an allow_unsafe_interrupts=1 option that was also related to Nehalem broken Chipsets. Basically, you have trying to use early era Hardware that was quite buggy, so is expected that Passthrough would be problematic. Have fun!
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