Trying to follow this thread, it is not clear whether the problem is with the cyl stop or the hand. In the opening "the cyl stop doesn't quite pop up on two chambers cocking it single action" seems strange in that there is no relationship between individual chambers and the cyl stop.

Question seems to be that the cyl is not turning far enough to allow the cyl stop to get into the slot on the cylinder. If it's that and only two chambers are affected there is some difference in the ratchet. Problem with Colts as they wear, in advanced cases none of the chambers go to battery till the trigger is pulled. On a gun in initial wear condition, individual chambers could be affected just due to production tolerances. In either case some attention to the hand should fix the problem.