I sounds as if the Parallel PCIe card that you are trying to used is not supported.  Have you verified that this card is actually supported by the system?  If you remove the card will your system boot?  Lastly if you insert another PCIe card (such as a NIC) does the system give you any errors?

The DL180 G6 supports PCIe cards, it has 4 PCIe slots by default.  Here are the quick specs for that server http://h18004.www1.hp.com/products/quickspecs/13248_na/13248_na.html#Standard%20Features

Try using a different PCIe slot, maybe the x4 one.  Also try to verify that another PCIe card will work in the slot are you trying to use, there could be a problem with the actual PCIe port on the system board.