Is your butt "winking" at the bottom of your squats? If it is your squat that is contributing to your back pain, it is probably an issue of tight hamstrings causing lumbar spine flexion. Try stretching your hamstrings before squatting and after exercise and only going as low as you can without the "butt wink."
Here's another thread on the topic (wfs):
http://board.crossfit.com/showthread.php?t=7113&page=1