S-6 can centerline crack with too low of depth to width ratios as well. The tranverse restriant, as M-Squared mentioned, will increase with member size, and thin passes can pull apart (though it is unusual with CS). S-3 is an option, since it will bridge a little better, if you are doing grooves, but you might try heavier beads.
And although seldom (I've never heard of it) an issue with CS's, a low manganese steel could vary the Mn/S ratio leaving more S in the weld metal (even though it is still reported as <.025) as diluted from the base metal.
It could be acombined phenomena. Restraint, increased S from dilution, thin beads, etc.