Have you monitored the 5v rail on the board while testing? i imagine it's raising up/down too.....
I'd be looking around the onboard regulator oand/or any capacitors and diodes associated with mainly the 5v supply.

I can't see how digital chips have a varying LEVEL of logic, so i'm thinking it's more to do with supply voltage and not logic/chips being faulty.

my 2c ;-)