A thought - do you have oil pressure doing the test? If one bank was on the cold-start pin and one had pressure then the relative cam positioning could be different.
I'd suggest pulling all the spark plugs and spinning the engine on the starter in 20-30 second bursts until all the valve train quietens down and everything has pressure and then try the compression test again. Give each cylinder the same amount of revolutions when testing so that oil pressure is consistent.
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