Are sure neither of these engines are DOD? I'm seeing or imagining I'm seeing a pattern in compression between DOD cylinders.
Don't think DOD/AFM/VVT was available on the gen IV's until 05 iirc on the 5.3, 6.0 or 6.2L. By 07 think they were pretty much in everything, cars and trucks.
Buddy of mine is rebuilding an 03 LS 4.8L for his track car and pulled the motor apart first before dropping in into his car. Save himself a lot of money by doing this because we found cylinder #7 had a smoked piston and cylinder #5 had some ring issues on the piston. A few extra hours and about another $600 and this kid knows he's got a solid motor for when he drops it into the car.
But for both engines to be doing this, there is definitely a pattern that is being repeated here. Assume that the common denominator is going to be the use of the same parts on both engines. Start there and dive deeper once that has been either cleared or tested good. But I've never heard of an engine slipping timing and then going back into time with gear driven motors. Best of luck with the truck and the new engine bud.