Don't know about the "underwater" thing.

You might have starved them for Oxygen, even though there where shitloads of bubbles. Maybe they almost drowned.
6 weeks? Shit dude, I gave up on my clones on the 4th day. I admire your Budha-like patience.

I think it'd be best to let the stems hang above the water surface. When bubbles rise to the top, they "pop". With that pop, small droplets/spray of water hits the stems, walls, ceilings, etc.

Also, I think you should use air stones, to make smaller air bubbles.

Just my 2cents

-turtle420
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