A wild guess...
Do all the clones have the same number of nodes below the surface of the medium? What I'm thinking is maybe if you root a bunch of cuttings with 3 nodes and a couple with 2, the ones with fewer nodes have fewer rooting sites and therefore grow more slowly.
How stunted are we talking here? Slowpokey vertical growth, or bonsai like if you have an early rootrot or rootbound problem?