Start them in bigger pots, seedling roots run out of room very quickly in small cups, thereby stunting growth.
Simple really!
Ideally some thing about 4 inches across and 5 inches deep, this is adequate for up to three weeks of growth.
Have a look at my diary "cannabis conundrums" and in week 7 I have posted some pictures of a root system of a 3 week old seedling and this might give you an idea as to why having adequate sized pots for your seedlings is so important.
Hope this helps,.... Organoman.