Starting with the basics, is your saddle the right height? When I first got back into cycling, mine was about 3 inches too low, got really bad lower back pain - bike shop said apparently if your leg muscles can't work efficiently, you compensate with the ones in your lower back.
Next time it happened, it was due to the reach being too long, shorter stem sorted it out to an extent, but the bike in the end got sold due to being the wrong size..
Sorry, if all this is stating the obvious and your bike is set up fine anyway...