I don't know what pattern you're using, but this is the one I always use for my scrappy strip blocks:
http://home.pmt.org/~awalter/string.html. They are addictive! Remember, when you're cutting the strips, watch your ruler; no matter how hard you try, it keeps moving a smidgen. Maybe you could try this pattern the next time?
Also, for baby quilts, I like cotton on top and flannel on back. That way, flannel is next to baby, but you get ease of working with cotton.
Good Luck!