Jesus and Nicodemus might as well be speaking different languages. Jesus speaks of birth from above; Nicodemus is befuddled. Jesus speaks of the spirit as wind blowing where it will; Nicodemus wonders how this can be. They are like a creationist and a paleontologist comparing notes on fossils--they simply can't fathom each other. Their organizing assumptions are too different.
Here's when we sense that Nicodemus begins to understand what Jesus is saying: when Jesus reinterprets the story of Israel in the wilderness, drawing from the language that has oriented Nicodemus's life and thought. It doesn't seem likely, after all, that the series of puzzling metaphors Jesus begins with would push Nicodemus to understanding. But something clearly does.