I have the same problem on my x570 motherboard.PCI passthrough of some USB controllers got broken after 6.2.6.
I'm passing through two of my motherboard's USB Extensible Host Controller (same IOMMU group) to a Win 11 VM and I noticed one of them failed to initialize on Windows after a kernel update.
I tried a fresh Win installation to rule out any Window config issue. Same problem.
I tried an Ubuntu VM where it also used to work. Same problem.
It's broken on 6.2.9-1, 6.2.11-1 and 6.2.11-2.
It works correctly on 6.2.6-1 and 5.19.17-2.
So this seems to be related to any change between kernel version > 6.2.6 <= 6.2.9
Solved by setting
disable_idle_d3=1
on vfio-pci.