Since you are fairly certain its coming from the "vent", let me make some assumptions.
I'll bet that vent is in the ceiling of his room, and not the floor.
I would venture also venture to guess that there is attic above his room, not another living area.
I would also guess that if you walked the perimeter of you house outside, you will find a missing soffit vent or some crack where varmits are getting in, maybe missing facia or turbine vents.
Does the smell remind you of the zoo?
If all of the above are true, then you probably have animals in the attic. Raccoons, squirrels, Oppossum, cats and bats all love to nest in attics. I should know, I've had them all, complete with urine smell. They seem to love to urinate near the a/c vent.
If you go up in the attic when you notice the smell, you'll probably find insulation that has been wet and pooped on. If thats the case, seal the exterior entry hole first, then dig out the bad insulation, paint the drywall with Kilz paint on both sides, and re-insulate.
If not, here's suggestion #2.
Do you have a cat??? or a dog??? How many times have the kids wet on the floor??? If urine was on the floor in large quantities, it soaks into the subfloor/slab and carpet cleaning cant touch it. If thats the case, pull up the carpet, clean the subfloor and re-install new pad and old carpet.
Thirdly, as mentioned before, some cooling systems and refridgerators use Ammonia instead of freon. To determine if thats the problem, I would seal off the vent in his room for a few days and check for the smell. If it is refridgerant from the a/c, it will show up in other rooms instead of his. Then its time to call the repairman.
Lastly, some new types of blown in cellulose insulation have been attributed to that smell. Some suggest that its the flame retardent, but no-one knows for sure, as its so infrequent.
One thing I do know, and that is if this smell is so strong it burns your eyes and hurts to breath, its way to strong to be in. Call someone that can test the air quality if you cant find the source. I would try the mold remediation guys for suggestions.