I usually wait until the fourth or fifth set of leaves, by then the plant should be "on its way" and have a well developed root system. Next time, fill your cups right up, this will provide more room for the roots to grow and speed up growth slightly. Have a look at my diary "Holy Mackerel" to see a baby plant without any soil to show how long the roots get in a short time and this may give you an idea as to why having the cups filled right up will help your babies. Hope this helps,..... Organoman.