This explains a lot.

It wasn't too long ago we talked about how Justin Morneau wasn't just in a slump--he looked lost.  Well it turns out there's a good chance he hadn't "lost it", he was just being hindered by lingering pain.  He'd batted just .158/.257/.293 since July 28.

Justin has a fracture in his L-5 vertebrae, making this a lumbar stress fracture.  A lot of times these fractures are brought on by improper movement, like lifting, while the lower back muscles are already fatigued.  Because the L-5 is where the lumbar connects with the pelvic area, once you've got a fracture in that area as an athlete there's nothing you can do but rest.  Any quick or exaggerated movement is going to cause a bit of pain, and even if it's not serious pain it's something that needs to be looked after so that it doesn't become serious.  In very serious cases, unstable fractures can have screws inserted to help the fractures stabalize, but of course we don't want this to happen.

To explain how this kind of an injury works in detail, I'll quote from the Physio Room:

The lumbar vertebra consists of a round block of bone at the front, known as the vertebral body, and a bony ring at the back. Three bony 'process' stick out from this ring and provide a place for muscles to attach. The area that is affected by Spondylolysis is a part of the bony ring known as the 'Pars'. It is not clear why, but the Pars area appears to be a weak spot in the vertebra.

In healthy bone, if damage is not excessive, a biological process called remodeling occurs and new bone is deposited to heal the damage [of the Pars]. In order for remodeling to occur, the body must be given adequate rest to recover from the repeated loading that occurs during sport. However, if the damage is excessive and the remodeling cannot keep pace with the damage, then microscopic failures (fractures) occur.

Essentially, it's just something that needs to be monitored.  It's already been said that Justin needs three months of rest; no lifting, likely no physical exertion whatsoever.  As long as he's giving his Pars enough time to recover before exposing his core to "repeated loading that occurs during sport", he should be just fine.