Is the medium having a chance to dry out at all? If it happens to contain peat - which many seedling/cloning mixes do - then it might be soaking up too much water, preventing oxygen from getting to the stem. I've never personally tried the 'bubble cloning' method, but I'd imagine you would have to be extra careful when using any kind of soil-like medium along with the standard nutrient solutions, air-stones/wands, etc., so that the medium isn't staying totally saturated.

Also, you might consider moving the unrooted clones a bit farther away from the lights. Rooting clones really don't need much light at all, since the focus is less on foliage production and more on developing a root system. I usually have no more than 2 32W CFL's hanging about 20+ inches over the tray (which can hold roughly 50 new clones in Jiffy pucks), and have never, at least to my knowledge, suffered any problems due to lighting. I have, however, experienced problems when trying to root clones when temperatures were too high. You mentioned using a heating pad, but didn't say anything about ambient temperatures, so this may or may not have had anything to do with it.

Sorry to hear about the clones, though. I'm sure someone will drop by who has more experience with bubbler/aero cloning methods who might be able to offer some other opinions.

Best of luck in the future. :thumbsup: