PCIe negotiated as x1 instead of x8

No! Whoops! I looked too quickly at the board schematic (for the wrong board, the Arria GX, to boot) and mixed up PERSTN and PRSTN. If A1 and B48 are connected than your board is at least being represented to the computer as x8 compatible, and so the problem exists elsewhere. Unfortunately I have no idea. I knew the solution above would be a stretch, that you probably had it configured correctly. Something is going wrong during link initialization & training... maybe the test out signals can help you. There are a ton of outputs there that can be used to diagnose physical lane errors, based on training sequences and ltssm states.