We have installed a new system and all new duct work and after 2 years the home owner has started to notice that she is getting black sute around her air supplys but not so much around the returns. The furnace is propane and the burners all look fine.

Dirt? If so the filters are not doing the job.

Check the furnace/duct discharge area for CO. It is possible the heat exchanger has a crack but not likely because of young age.

If mold check to be sure A/C drain is clear.