I just saw this post, so sorry for the late reply. Before my son's sophomore year (2007) he had a similar issue. it is a repetitive motion injury also called spondylolysis, which is a defect in the pars interarticularis. My son's was with the (L5) and was bilateral (caused by both batting - hits left and throwing - throws right).
This can be plenty debilitating and will not go away unless properly treated. Typically you need to see an sports orthopedic doctor who deals with children (sports pediatric orthopedics) and it is helpful if they have dealt with this type of injury before (not all will have). X-rays or an MRI will not typically show the injury, a CT scan almost always will (likely you will need to push to get a CT scan).
After healing, PT must follow to further develop the core and hip flexors prevent a return of symptoms, or they will likely return. We went through a very frustrating time with this injury until my son received the right type of PT. We actually had my son go to 4 different doctors before we found the right one. So, if you are not getting the answers you need, look elsewhere.
There is plenty of information on this if you look up spondylolysis on this site. As well, this post may prove helpful: http://asmiforum.proboards.com/thread/1100
The good news is my son totally recovered from this and is currently entering his senior year in college, as a D1 P/OF. He has had no further issues.
Best of luck and please reach out using the dialog feature (PM) if I can be of help.