Just because it has the same dish doesn't mean that the compression height is the same on the replacement pistons as it was on the stock ones. You could have one piston that wasn't right and is sitting higher in the bore than the others.
Also, you said you bought a head that was already assembled, did you remove the rockers from cylinder 3 and rock the valve to see if it moves? Maybe there is an issue with the guides on cylinder 3.
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