MKO, if you are able to disable the device in the guest prior to VM shutdown and that fixes your problem, what you can do is write a simple script that disables upon shutdown and enables upon startup. It's what I do for my graphics card. If you can verify that works I'll write up the process...
I'm not sure you're going to find SSH OOB management on any of those boards. Pretty much all of them use the exact same BMC (AST2400), which I don't believe offers what you're looking for. You're better off enabling SSH on a Raspberry Pi and running ipmitool from there.
I know that ATI cards have trouble starting back up when a proper PCIe bus reset hasn't occurred (like you would normally do running bare metal). Indeed, this is the issue I would see with my VM: the first time you start the VM after rebooting the host, no problems. If you restart the VM, the...
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