Sigh... Unfortunately, jag, that is one of the great unanswered questions. We do know however that without an intact pain system, people start to damaging themselves immediately. Without pain we do not know how to avoid damaging our bodies. People born without an intact pain system do not live long. We are not allowed to modify the pain system very much.
Soft tissue injury. To my mind, reason for most chronic pain is chronic soft tissue (fascia, muscle, tendon, ligament & nerve) injury. Despite what lay people believe, ct & MRI scans provide less than precise architectural views of these tissues. Within the arena of medicine there is improper conduct that "if it cannot be seen or measured it does not exist". This is why we have an epidemic of chronic pain in U.S.