Yes, your hens could have had the ms from birth. They might show no symptoms until stressed. Also it could have been brought to your flock by eggs, clothing, shoes or wild birds. I have a closed run but a bird could have flown over and dropped a feather or poop. Then it would have been there. The first stages usually show resp. sneezing. Then the other symptoms appear in the hens later as the joints are more involved. Its a lot like arthritus in people but much more serious down the line. It is very contagious.
This is what I did. Num. one culled my entire flock! Then took out all bedding, put in a real floor, scrubbed everything with vikron-s. I sprayed the soil in the run also with virkron-s. It kills viruses in soiled areas better than clorine. The Ms dies after about two weeks on surfaces but last longer on manure and feathers. I also added fresh sand to the run that I have covered. The rest I limed well and planted alfalfa seed. I painted the inside and outside of my coop and cleanned everything again with clorox. When dry I added the bedding. I waited three months and got chicks from a source that had hers checked 3 months before for the disease. Also I ordered Denaguard. Its an antibiotic used for swine etc. that kills this particular virus. Experimentally I am using it at the rate of 8cc a gal in their water x three days in a row every two to three weeks to prevent re-infection. So far so good. I have not had them checked as they are only now 4 months old. They will be checked soon.
That was such a sad time for me and I miss my sweet hens I had before still. I still have their pictures. They were good layers also. I so hope this helps some. Gloria Jean