Fitness, the callsign for the flight is composite, i.e. the flight callsign is Cobra-1 and then each individual element in the flight has it's own no. You can see this when placing an aircraft. It allows u to pick both the name and numerical components of the "flight" callsign.
So, lead will be Cobra 1-1, his wingy Cobra 1-2, etc..
However, as I have no military background I have no idea y this is so. To fathom a guess I'd say it was either due to the often large number of sorties in the air at any one time, or to allow the "packaging" of flights, i.e. Cobra package composed of 3 flights, cobra-1 on SEAD, Cobra-2 on A/A and Cobra-3 on strike?