are you using a medium in the top of the cloner, or is it the neoprene sleeve type? if you are using a medium, you could try a rooting agent (gel or powder) and see if that helps. i have had success with the gels in the rockwool i have in my cloner.
but most importantly, as Onyx said, make sure that your water is pH adjusted. if the pH is too high, it won't matter what sort of nutrients you put into the water, the plants on't be able to absorb them (or so i read).
good luck man!