I've experienced this issue myself and I saw some people complaining about it 
on the mailing list. Sometimes Qubes takes forever to poweroff.

The issue is caused by the fact that for some unknown reason machines with PCI 
devices attached take forever to shutdown and sometimes need to be manually 
killed from within VM Manager. After manually killing them, the system will 
shutdown normally.

So, here's the fix:

In Dom0 run qvm-prefs -s sys-net pci_e820_host false

Repeat that for sys-usb and any other machine that holds a PCI device.

Your system should shut down normally after this.

No, I don't know how or why this works but I know that it solved the issue on 
my machine. Explanation welcome. I'll add this to documentation once we have a 
confirmation that this is 100% reproducible.

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