Yep, that's exactly it, different strains. The sore mouth vaccine doesn't prevent them from getting it anyway...It gives it to them on purpose, but only one strain of it.
The sore mouth is in the ground of your property. It can live there for many years in our climate. When I got into breeding again after a break I opened a building that had been shut up for 8 years...Guess what, the sore mouth from the bummer lambs I used to raise in there was still active.