I've had patella alignment issues...it hurts and sucks. Go see a physio and get a really knowledgable personal trainer. All can be fixed but get on it early.

My issues stemmed from a the tight muscles down the outside of my thigh and a poor running technique (I didn't engage my glutes enough). Bear in mind I only weigh 73-77kg's and compete in endurance running/cycling...so it can happen even when your body is somewhat conditioned to fitness.