Here's the update:
I have a GA-EX58-UD5, with a beta BIOS that supports VT-d:
http://ggts.gigabyte.com/FileList/1134809/ex58ud5.13s
I also have a Xeon E5570, just to be extra sure VT-d is supported.
I'm using Debian latest with Proxmox installed, and as such I'm following this doc:
https://pve.proxmox.com/wiki/Pci_passthrough
If I DO NOT enable VT-d in the bios and boot with the intel_iommu=on parameter in grub.comf, I am able to boot. When I get to a console, I can see IOMMU and DMAR:
dmesg | grep -e DMAR -e IOMMU
[ 0.000000] DMAR: IOMMU enabled
[ 0.029681] DMAR-IR: This system BIOS has enabled interrupt remapping
But when I run the "dmesg | grep ecap" command, nothing gets returned, indicating something is wrong with IRQ remapping.
Similarly, I get nothing back form "find /sys/kernel/iommu_groups/ -type l", so this setup is definitely not right.
If I enable VT-d in the bios AND leave in the intel_iommu=on grub parameter -- as instructed in the official doc -- I get a hardlock very early on in the boot, just like with the Rampage II Gene / ci7-920.
As a third option, I leave VT-d on, and remove the intel_iommu=on parameter. In this case, not surprisingly, IOMMU is no longer enabled, but DMAR is much busier:
# dmesg |grep -e DMAR -e IOMMU
[ 0.000000] ACPI: DMAR 0x00000000CFEE94C0 0000B0 (v01 IntelR AWRDACPI 322E3030 DRWA 00000002)
[ 0.029719] DMAR-IR: This system BIOS has enabled interrupt remapping
[ 0.714911] DMAR: Host address width 36
[ 0.714913] DMAR: DRHD base: 0x000000fe711000 flags: 0x0
[ 0.714927] DMAR: dmar0: reg_base_addr fe711000 ver 1:0 cap c9008010e60262 ecap f0207a
[ 0.714928] DMAR: DRHD base: 0x000000fe710000 flags: 0x1
[ 0.714934] DMAR: dmar1: reg_base_addr fe710000 ver 1:0 cap c90780106f0462 ecap f020fe
[ 0.714935] DMAR: RMRR base: 0x000000cfef0000 end: 0x000000cfefffff
Although I do now have remappable interrupts, as demonstrated by "ecap f020fe" and "ecap f0207a" above (specifically the trailing character a-f), just like with IOMMU enabled and VT-d not, I have no IOMMU groups in /sys/kernel/iommu_groups.
I'm out of time for the day, and I'm not sure where to begin troubleshooting tomorrow. It seems that I can have either iommu or VT-d enabled, but if I enable VT-d then I cannot have iommu.
I know people have gotten this working, with this MB, and in Linux as well. Tomorrow I'll start looking into bugs. I read in another thread that vfio on X58 can be a problem with some linux kernels. Since the kernel didn't change between servers, I'l leaning towards the problem being somewhere in there.
This probably deserves it's own thread again now, but I wanted to update this one too.
Thanks in advance.