Cyclone V SoC Rootport with MSI Ref Sys limitations

Hello, I am trying to get the Cyclone V Rootport with MSI ref System (Ref Rocketboards) to enumerate a PCIe x4 Endpoint with no success. I have tried the Intel CT NIC which is an x1 Endpoint and it enumerates fine. Any similar experiences or known limitations to share? Thanks, Mounir