I have created a 3D project, added a terrain to it. Textured it. And added an FPS Controller from Standard Assets. I run the project. It working perfectly. Okay, now I have raised the level of terrain on some part and played again. But the problem is this time the FPS controller is behaving as if the terrain collider is flat as before lowering it. Please watch the attached video which shows the problem (I could not attach it here. So I uploaded it to a website. Link to video: http://uploadanotherfile.ml/d/Unity_Issue_Terrain_Collider_Flat.mp4)
Note: I placed the FPS controller above the terrain running each time.