I missed "you" in title. Please tell the difference between "Why aren't you...?" and "why are you not...?" For example: "Why aren't you telling me" and "why are you not telling me?" Please explain these two structures and their meanings.
"Aren't" is a contraction. There is no difference in meaning. Most people use the contraction when speaking.
It's possible that someone would say "why are you not telling me?" if they wanted to emphasize the "not."