Is it just because the air they are going through is more humid than the surrounding air so when they leave that patch the cone disappears?
You'll want to check out NASA SP-514. In particular Chapter 2.
The vapor cone you see is actually a cloud. It is condensation of vapor into tiny water droplets when the temperature and pressure are just right (based on the local humidity).
So, changes can occur due to local changes in humidity and temperature -- but the biggest effect is changes in pressure due to the aircraft. For example, sometimes the condensation only occurs when the aircraft is "pulling g's" -- it is highly loaded during a turn or other maneuver. During this state, the aerodynamics are working hard -- which leads to more extremes of pressure and a greater likelihood of condensation happening. However, the pilot doesn't sustain that maneuver for a long period, even relaxing a slight amount can make the condensation vanish.