You may wish to discuss your concerns with your son's motor gait with school personnel, such as the gym teacher or a physical therapist. You may need to request in writing for a formal meeting to see if there are any concerns with his physical milestones.
Regardless of his manner of running, I applaud that your son is exercising!
Without a video this is a tough question to answer; however, pre- pubertal boys often look like their female counterparts because they use their arms for balance and work them in the run. As boys age, they use leg muscles more efficiently and tend to put legs forward and chest straight. It is a matter of time, practice, and body build that may change with growth. Both can be very skilled runners.
Wayne Yankus, MD, FAAP
expert panelist: pediatrics
Every person balances themselves differently. Some of that comes from a physiological standpoint, i.e. the actual structure and function of the different involved body parts. Some of that comes from mannerisms and personality that is inherited from environmental influences, like the people around them in their lives like friends and parents. My personal situation with this is that I've collectively broken my ankles five times and I walk and run on the balls of my feet, and walk slightly pigeon-toed. I walk like a woman in heels and run like a girl. Maybe some of my doing this comes from me relating better with women as opposed to men as well. Take a look at what might be affecting your child, because these are things that might be a factor in what is causing your child to "run like a girl".
How does a girl run? If your son's body placement during running does not "look normal", check with his doctor. He may need physical therapy to strenghten a muscle group or could be an orthopedic situation, too. Or most likely it is YOUR problem having a son that displays effeminate physical traits.