Having the same issue. Even tried the narrative.start_narrative narrative_strangetown_act4 cheat, which didn't work.
This alters my game saves, too.
First off, I do have mods installed. I always have. However, the file that I first played and completed with StrangerVille reverted to normal after the defeat of the Mother Plant. This was completed about 5 days after the pack was released.
I beat the StrangerVille mystery in a different save file recently. The mushroom cloud and all of the plants remain, even during normalcy. I have since checked the first save (which I reset to strangeness months ago) and the cloud will not not go away, even when normalcy is requested.
Both of these saves are clones of an older mother save prior to StrangerVille. This problem appears to be recent.
So far in my new save, StrangerVille has no cloud, however I've yet to actually play the mystery there.
