Dev Kit and Dell "Training Error"

Sounds like Altera's problem and not Dell's.

We have very similar problems on Intel S3420GPLC motherboard which is completely different from your AMD-based Dell in just about everything.

PCIe part of Stratix-IV GX devkit is simply broken. If something appears to work for you in some other PC that's probably because the chipset in this other PC doesn't check the replies from devkits as thoroughly as server-class chipsets in S3420GPLC or PE-6950.

BTW, which of PCIe core variants did you test - hard IP or soft IP?

In our experience both are problematic (and almost certainly non-compliant with PCIe standards) but soft IP is less problematic than the hard IP. Soft IP not always trains to desired width (x4 in our case), but at least when it manages to trains correctly it works correctly thereafter. No such luck with hard IP variant that hangs the whole system during majority of attempts to change the power state, including system restart/shutdown.

I wonder whether the PCIe problem is only of devkit or of the whole Stratix-IV GX line. In later case Altera is in deep trouble.