I've also been doing the starting strength program for the past two weeks and I've also been experiencing lower back pain. I think its just because I never did deadlifts and squats before now and my lower back muscles have been under developed. I'd say to first make sure your form is correct on the excersizes. I found videos of how to perform them correctly on youtube. I've also takin Potassium supplements and L-Taurine supplements to prevent the pain. It may just be cramps from not having the correct balance of water in your muscle cells, Potassium will prevent that, eat alot of bannanas. Taurine also helps with the pains and cramps as well, Ive been taking both and the pains have diminished. I also believe that by working your ABs which is an opposite muscle group may help releive some stress on the back.

I'm new to this so i dont know if what I said is correct, It's has worked for me though. Hopefully someone more knowledgable will either renounce or support whit ive said.