What’s happening is that any texture/tile that is for concrete, asphalt, etc, is global - that texture will override MSFS default texture. No mods/freeware should replace the actual texture file - unless you put it there deliberately. 
So for example, if there’s a specific concrete texture file for KSAN and KLAX, a freeware for KJFK using that same texture file will override all textures of that same file name.
See if removing the freeware solves it.