Problem with configure Stratix III with AS using EPCS128

It's sounding more and more like a signal integrity issue, although 1-2cm is nothing to worry about.

Your scope plot doesn't look particularly reassuring. However, with the probe in contact the device configures? Is that right? If so, then the actual signal quality is not that bad. Any chance you can connect to a more local ground connection? Ideally, a soldered ground connection near the probe point. That will improve the trace somewhat.

Is this board a one off? Do you have another to try?

How good do you're power rails look? Check them all but specifically, VCCPGM and VCCL. VCCBAT isn't floating, is it?

Cheers,

Alex