UPDATE:
Going through my theme project folders, there were explorerframe.dll and explorer.exe that I modified. And I have forgotten about that. Now everything makes sense. I actually used Theme Resource Changer before. Why it slipped my mind, I don't know (must be the name of the application which can easily be mixed up with something else). So right now, I'm sticking to three programs to create a theme which I believe will get rid of the clutter, overcrowding and depedency to more programs:
1) Resource Hacker Fx
2) UxStyle Core (will get rid any concern with windows updates)
3) Theme Resource Changer (will put an end to relying on StartOrbz, W7 Navigation Button Changer, etc.)