I can empathize with your stepson, because I've also been having a tough time with fall allergies, as I wrote about in my most recent post here.  I find that even while new allergy medicines help, those pesky allergens still manage to find a way to cause problems. 

The best thing to do is to discuss your concerns about your step son with his doctor (or have him do it if he's old enough).  There are still other medicinal options available to you, as you can see in this post.  Another option to discuss with your doctor is allergy testing and allergy shots, if you haven't done so already.

Obviously I can't diagnose your stepson, yet what you describe here makes me wonder if perhaps your step son might have exercise induced asthma or asthma in general.  If this is the case, asthma preventative medicines might help. 

At least these are some options to consider.  Either way, you should definitely have a discussoin with his doctor, because there are options.