Closed chamber with flat tops

That's whay I'm talking about tho - there is no difference in distance from valve to piston between open or closed chamber head designs. To me, the fact that it's only one or two cylinders says it's not a consistent issue. Chances are they are at least .040 down, and the gasket is the same thickness. The cam is not lifting the valve much - the "normal" max for a small block is around .520 lift. Even with 1.6s I don;t think you're there.
Regardless - if it's apart get yourself a dial indicator and some play dough and measure how close they get on a few holes.