Clonex has no fungicides in it, while all the powders I've seen DO.
I think it is likely you are having fungus problems.
Do you sterilize your propagator between uses?
Just FYI if you want a liquid with fungicide, dip-n-grow is my new favorite grow product. WOW does it ever work.
Clonex goes bad after it has been open for a while, so if you see a sudden drop in % rooting, that could be a culprit too.