Cyclone VGT Dev Kit boards - some new boards failing to boot from NOR Flash

That's rather disappointing to hear, actually. The Max V design is Altera's design. One of the boards fails to boot with multiple retries even with the factory binary. 

If I remove the factory_user input inversion (a simple NOT statement) then the factory Max V design fails on 5 out of say about 20 boards, since Rev B boards came out. Why? I am not convinced that these new boards are identical to the working ones, sorry. 

I suspect the "pass/fail" OQC for these boards includes checking that they configure without error, but under the hood, some of them are failing and retrying configuration multiple times. At the performance of the parts on board, a single configuration failure is a board failure. I suggest the factory bootloader be reconfigured to fail at one single retry, then you will notice the board issues before shipping them out. 

This Max V design is Altera's loaded up to 99% utilization. Not my doing. 

In short, I have a new build that "works" with the new boards, but no evidence as to why. None of the timing reports on a "failing" design are showing up with errors, they are just mildly different from the "working" design. 

I am not pleased with this outcome at all, sorry to say.