I had similar problems with a DL380 G6 after upgrading to Fangtooth recently.
I used:
midclt call system.advanced.update '{"kernel_extra_options": "intel_iommu=off"}'
…to add the intel_iommu=off kernel parameter. When the systems boots you can see that the kernel parameters include both intel_iommu=on and intel_iommu=off, the latter overriding the former.
FWIW, I also turned off Intel VT-d in the BIOS, just in case the kernel parameters ever get reset/overridden by an upgrade.