EPC16 does not configure EP2C35 at high temperature

Generally, I must admit that I never used an EPC device and thus don't have any experience regarding it's particular behaviour and don't know, if there are hidden design traps or known issues.

From the reported observations, the problem seems to be caused by the EPC16 only, but I don't see a point how to localize it further. The previous comments on possible soldering, power supply, bypassing and grounding issues should be checked to my opinion. But it's hard to decide if these are more or less likely without knowing the design details and having the board at your fingertips.

As another comment, the (working circuit) waveforms don't look really good, the overshoot, if actually present with the shown amount, is considerably exceeding the FPGA maximum voltage range. I guess however, this may be a simple probing problem. If the design has long signal traces for the respective signals, the overshoot could be real and you're missing a source sided serial termination. But I don't think that the no-operation is related to this waveforms.

Good luck,

Frank