I built a bubble cloner probably very similar to yours (although a pic or two of YOUR cloner/light setup here might help folks here with diagnosing your problem), and have used it multiple times under T12 fluoro fixtures. I keep the top on just to be sure that humidity stays high enough, but you could try taking it off for a while and see how your cuttings look. In my experience, cuttings that are properly situated in a bubble cloner (bottom of cutting just above the water level) may look droopy for the first few days with or without a humidity dome....but should perk up afterwards (even before they start growing roots).
I would also recommend trying just plain tap water with NO nutes and NO rooting gel. I've never used Superthrive, so I dunno, maybe it helps...but I've had 100% success rate using a bubble cloner with just pH-adjusted tap water and nothing else.
Also, be sure to give it enough time. Although lots of folks here report 7-10 days for rooting, I usually have to wait two weeks for consistent root formation...and often three weeks or more before ALL the cuttings in a batch have successfully rooted.
Finally, that 400w lamp is way more than is needed. While I doubt that its the reason for your lack of success in cloning thus far, it probably couldn't hurt to get yourself a cheap 20-40w cfl bulb (preferably 6500K or 5000K) and just hang it directly above your cloner (maybe with one of these
http://www.homedepot.com/h_d1/N-5yc1v/R-100664506/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053). Fluorescents are IDEAL lighting for cloning...so, if you continue to have problems getting roots under your 400w, why not invest $15-20 to have a light setup that's perfect for what you're trying to do?
Just be sure to have PATIENCE, and give your cuttings at least three weeks before you throw in the towel. Could be that the strain you're attempting to clone just takes a little longer. As long as the conditions (pH, temp, humidity) are reasonable, you should be able to keep cuttings "alive" in your bubble cloner for many weeks.
Although I still have my bubble cloner, lately I've been using rapid rooter plugs (
http://www.hydroponics.net/i/111400) instead (again, with no nutes or rooting hormones). Usually takes a little longer to get fully rooted clones (about three to four weeks), but I just stick them in a clear tupperware tote with another one upside down on top and pretty much leave 'em alone. They never look as nice as the ones in the bubble cloner while I'm waiting for roots to form (they tend to look kinda droopy the whole time), but given enough time they always root, and I don't have to bother checking/adjusting pH at all...I just open it up every few days, and mist them maybe once a week. Works great. As I said, though, oftentimes they look like they're practically dead before I start seeing any roots coming out of the plugs...but they somehow survive and form roots EVENTUALLY every time.
So, if you continue to have no luck with the bubble cloner, you might wanna try the rapid rooter method sometime.
Good luck