When it asked you all those questions that first time it was using your answers to generate its own .config file.
Just now, when you copied the proper .config file over, it would have asked you if you wanted to overwrite the .config file that was there. You should have chosen yes. Did you?
If so, then you probably need to start over with the fresh kernel source. Make only compiles when it thinks it needs to, and it sounds like it doesn't think it needs to since you have just compiled already.
Working with the kernel can get annoying.