I can see what you mean. I have not noticed those in Skyrim. But I do not apply any mode other than by Nexus Mod Manager.
When you say you reinstalled the game, did you leave out the mod or reinstall it too? If yes, better to just leave the mod out of the game if the moving shadows persist. Probably a bug in the mod. Better chance of getting more support from the modders themselves.
By the way, I still do not have the mod to add a new City as you have. Can you share the link to this.
But I deleted the mod, so i cant be that!
- Sorry, can't find it