Possible reasons for BIOS not initializing the PCIe BARs in Stratix4GX PCIe HardIP

I am trying to understand possible reason on why sometimes the Base Address Registers in Stratix4GX HardIP is not getting initialized. I did the PCI device serach and it is able to find the Stratic4 GX PCIe hard IP. But sometimes the BIOS is not initializing the Base address registers. What can cause this? Is this a 100MHz reference clock or reset issue? But if so why it is able to find the device?