If the chips are from the same lot the internal timing of the chips should be the same. Reading this (although still difficult to imagine your tests) it seems you have an oscilator problem. Couple of possibilities: there is a frequency drift/variation, the oscilator is running at one of it's harmonics (incorrect decouple caps's) or the signal from the oscillator is not correct causing the controller to "miss" clock pulses. Me bed would be on option 2...