If you are using the stock Atlantis, then look inside your MESHES folder. There should be another folder inside called ATLANTIS. Look in there. There should be 4 mesh files in there...
~AtlantisVC_lo.msh
Atlantis.msh
AtlantisCockpit.msh
AtlantisVC.msh
If they are present, then open each of those files. At the end of each file, there's a list of textures used by that mesh.
Write down the names of the texture files used by each mesh. Then doublecheck your TEXTURES folder to make sure that each of the texture files is present.
If all are where they should be, you might also check your scenario file and make sure that the required Sol system is called out on the SYSTEM line of the scenario file.
Different Sol systems are used by different add-ons to display the correct environment for the add-on. I have 3 different configurations for KSC/Canaveral and all are visually very different. Though all use Kukanotas' Hi-Res surface tiles, 1 has all of the pads & gantries for missle row, but no 39A/B. One has 39A/B as they appeared in the Apollo era and the last depicts the cape as it appears today. Each is called up by the Sol system entered in the scenario. If the wrong one is entered (or I use a scenario not designed for that add-on), the wrong layout will be displayed, which could include missing launch pads.
If all else fails, you may be looking at rebuilding slowly on a clean install. But check each add-on as you install it so you know where the conflict is and can more easily correct the problem.