Re-reading the manual and following the initialisation procedure..
I have got as far as setiing up the SerDes, taking PCI out of reset, setting Outbound window and configuring the CSB registers the PEX_LTSSM_STAT status code returns 4 then 8 but never returns 16.
Code 8 is Polling Compliance, does this mean it is having trouble communicating across the transmission link.
This link is on a new card so is unproven.