Proxmox GPU IOMMU passthrough messes up shutdown

I have taken a spare Lenovo M920q as a additional virtualization server. I installed Proxmox and prepared the Passthrough of the APU (Intel HD630) and it is working fine, however, when I shutdown the node either via the proxmox interface or via cli (shutdown -h or halt) the onboard V-pro (Intel AMT) management stop working (that is, I can no longer reach the IP address and even the ethernet onboard LEDs turn off). It appears that the shutdown turns off also the vpro module.

While troubleshooting I reversed the passthrough and noted that if I do so, the shutdown works fine while still leaving the AMT module responding.

To use the passthrough I have the following parameters on the /etc/kernel/cmdline:
intel_iommu=on iommu=pt i915.enable_gvt=1

Does the fact that I use IOMMU make the shutdown go to other S-level? Has anyone noticed something similar?
I did update the bios and AMT to the latest version from Lenovo Vantage.