The problem is that the surface tiles are moved respect from scenario.
Since tiles can't be moved, the only option is to edit scenarios to make them fit.
There is nothing wrong, it is a known issue since it was released long ago.
To me, the choice is:
a) To have those hi-res textures
b) To have vessels in place
Another issue you will have is that some scenarios will cause crashed to desktop because of the pad definitions.
Also, just like in the stock KSC you may find buildings placed on roads.
I made a fix
http://www.orbithangar.com/searchid.php?ID=2868That will not give you the CTDs for pad definitions, and that relocated KSC base so it does not interfere with roads.