Sounds like too much heat or light....but...

1. Did you soak and rinse the cubes before use, with properly ph'd water?
2. Have you tried propping them up?
3. How warm/hot is it inside the propogator?
4. How close are the lights, and what kind are they? (CFL, MH...)
5. Are you misting with plain, ph'd water?
5. How large are the shoots you're trying to root?
6. Did you use the rooting hormone sparingly? (more isn't better)
7. Once cut from mother plant, did you work quickly to get 'em in the cubes?

Personally, I cut the clone a bit long, then just before dipping in the gel or powder, I'll make another cut while underwater, so any suction caused will uptake water, not an air bubble. (water is ok...air is not ok) Then I dip, plant (I clone into potting soil) cover and wait. I then mist the lid, not the clones. A few times a day. Some folks mist with a very weak solution of Superthrive, or other micronute after a few days, but I don't. Takes a week or so to start seeing new (pale green) growth.