The main difference between a cajon and a flamemco cajon is the snare.
Traditional cajons were simply a wooden box with a thin wood playing surface. But the flamenco cajon has the addition of snare wires running up the the back of the playing surface to produce a rattle or snare sound.
The flamenco cajon came about when Paco de Lucía (flamenco guitar player) went to Peru. He was introduced to the cajon and and he took some back to Spain with him.
He then ran guitar strings up the back of the front playing surface of the cajon and the flamenco cajon was born.
Further inovations to the flamenco cajon have seen a drum snare used instead of guitar strings, and many different ways of adjusting the snare or strings to give a tighter snare sound.
Most cajons which are sold these days are in fact flamenco cajons as they feature an internal snare mechanism.
The introduction of the snare gave the cajon a much wider variety of sounds and thus led to the instrument being played in more styles of music.
Today cajons are sometimes known as "A drum kit in a box" because the top end of the cajon can be used to replicate the snare drum while the main body gives a bass tone and with different hand techniques many mid tones can also be achieved all from the same instrument.