I checked the design for any pins configured as outputs or bi-directs having potential to be fighting another chip, both at power up and after reset goes away and board operation begins. I didn't find any.
Hard to say about how my cycles to cause it, I would give it a range of it happening on the 20th to 100th power up. I would say we have had this happen 8 or 9 times. We only have 7 cards total.
I configured Quartus to set all unused pins to inputs with pullup.
Parts have been configured when the event occurs.
I is cumersome to run boards from 3.3, but may need to revisit that.
I agree, purposely raising 3.3v up to verify that duplicates the failure would be nice, but to destructive with small number of boards we have.
Good ideas, keep them coming.