Aero/bubbler/DWC cloners have this habit of rinsing off any Clonex gel which remains on a stem that's been dipped in it. NT suggests soaking the stem tips in Clonex gel for 15-20 mins before putting them in the cloner. I can't suggest anything better- seems to me that soaking the tips for a while will give an oppty for the gel to be taken up into the stems where it won't be simply rinsed off.
Keep in mind that rooting gels and powders are not essential- they will speed things up but absence of the stuff won't stop rooting from happening. The plant is programmed in its DNA to send out roots when a damaged part of a stem comes in contact with the right level of moisture. It will set root anyway, with or without rooting gel or powder. It'll take a bit longer without the stuff, though.
I have used Clonex gel before, but I prefer powders when cloning in rockwool. Powders form a paste which stays put in rockwool better through several waterings, but the powder will wash off in a DWC/aero arrangement as easily as do gels.
Pathogens like fusarium and pythium grow very easily in plain water. Stem tips will rot and the plant won't be able to get any water. The H2O2 eliminates the pathogen problem and adds oxygen to the solution in the cloner.