Hmmm...it's a long shot but Corprus does confer a sort of immortality - resistance to all other diseases, though it does leave insanity and hideous deformity in its place. And if the stalkers were Dunmer or Altmer (if that matters at all) before they were infected, that means that they would also have about a 1000 year lifespan. So, theoretically, it might just be possible that some of the original corprus monsters might still be alive after the events of Morrowind.
Or a different idea: Vvardenfell is much different place now that Red Mountain has erupted. I've heard people ingame talk about how horrible and desolate it is now - a wasteland of ash and fire. What if the volcano's eruption blasted some remnant of Dagoth Ur's evil into the air, creating a new generation of hapless corprus-infected victims?
