I'm not sure if I'm 100% on topic or should start a new thread, but I recently upgraded my x370 board and things have been interesting. I have an Asus Prime x370 Pro which was working fine with my Ryzen 1700 for a long time on an older BIOS from 2018, with decent IOMMU grouping for USB passthrough to VMs. I ordered a Ryzen 3900x and upgraded BIOS while I waited for it to come in the mail, and ran into the same problem as Spaceinvader One in the video below. (I think this is what @mhentschke is getting) Luckily, plugging in the 3900x mostly fixed things, but my IOMMU groups totally changed (I don't have a single usb controller that's in it's own IOMMU group anymore, so that sucks). It sounds like for that part of the problem, the solution is either upgrading the CPU or installing the custom kernel per previous posts.
After the BIOS and CPU upgrade hardware addresses for some of my devices changed and had to be updated in the VM XMLs for things to work. For example, an address that used to direct to a discrete USB controller I installed turned into some other PCI bridge or something, and that was listed under "Other PCI devices" on bottom of the edit VM page. I suspect this was part of the problem @klingon00 described, the other part being the AMD reset bug causing his GPU to hang after having a VM crash and having to force stop. BTW, Klingon00, I would manually check your hackingtosh XML, as I know with my setup based on a Spaceinvader One tutorial, if you change anything at all from the GUI menu it deletes some of the special QEMU arguments that let the MAC boot.
Now, what I'm getting is my two windows VM's with nvidia cards passed through still work fine, but I've tried to passthtough the secondary card to a Mac VM and several linux distros including the latest stable Ubuntu 18.04 LTS, and all will apparently crash on boot and just give me a black screen/no signal. The monitor will actually go to low power mode, and I can't remote in via splashtop, so I don't think anything is actually booting.
It seems like this all could be related to Ryzen 3000 BIOS update issues, but if anyone has any hints for me about why GPU passthrough would work for windows and not linux/mac, that would be awesome.
I think the next thing I will do is try passing through GPU on linux VMs with different machine types and switching between SeaBIOS and OVMF.
Sorry for the novel, but I'm really suspicious that all these different issues have the same root cause..