Is it while you're exercising or after you're finished? I have scoliosis as the result of breaking my hip when I was 19, so I have a lot of lower back pain when doing squats and dead lifts. The only thing that helps is having a wider stance when doing the squats and either stopping or ignoring it when I do the deadlifts. It always goes away when I stop that particular exercise. And BOY - those lower back stretches in CTX back are awesome! Maybe you should try doing those more frequently?
Could be that you need better shoes, too. I was having a lot of back, knee and ankle pain until I got new sneakers.