I too ran into this issue passing through an LSI 9305-16i HBA to an OpenMediaVault VM after upgrading from Proxmox 8 to 9, where PCI passthrough worked great in v8, but failed in v9.
I updated the HBA firmware and bios (an endeavor), that didn't resolve the PCI passthrough failure.
I have the following kernel options set for `proxmox-boot-tool`: `intel_iommu=on pcie_acs_override=downstream,multifunction iommu=pt` and I have the following options set on the PCI Device passthrough options (a solution suggested above): `pcie=1,rombar=0`. However, these options didn't resolve the issue. As @FuzzyLobster and others mentioned above, the issue appears to be related to the kernel version. Kernel version 6.14.11-4-pve failed, but when I pinned to 6.8.12-15-pve, passthrough works again. Thanks all.
