I use loose well-composted lawn waste when potting cuttings (sometimes just shove the cutting in without pre-rooting), and those that survive thrive in a shaded  spot in the yard.  Those that perish are almost universally striped of the bark below the soil surface. 

I know at times the medium is too wet, but this aint rot, I think, but something being well fed.  The pots are well-wormed and likely have all the other compost critters large and small. 

Any thoughts on the culprit? 

someone here mentioned microwaving to sterilize some potted soil that I found contaminated by root knot nematode, and that may be effective here too.  Does anyone do this routinely for their rooted cuttings?

I have not had too, but have done so with orchid mix and would advocate it for those who find sterilizing advisable.

Fungus gnats perhaps?