I use rapid rooters - don't use the paper towel method first. Place the seed directly into RR's next time. The rapid rooters should be moist, not water logged - i use a spray bottle.
They could be reaching for light, or the light is too strong for seedlings.
Without a pic, it's hard to determine the cause or help to solve the problem.
If they're stretching, go ahead and plant them in dirt/pots (rapid rooters) covering most of the stem.