It can be various reasons why this happens. The best thing to do here is to consult with a physician. Just for your information, I know a large number of people who do or have done CrossFit who complain about back pain. The fact that it also hurts while running (another high impact exercise) could be an indication of some kind of damage or degeneration on your spine. This is the reason why I would strongly recommend for you to see your doctor.
I hope this helps.