The problem happens when you have 2 (or more) traffic*.bgl files that use the exact same (flightplan) schedules. This happens when the author uses existing flight plans, just substituting different aircraft.
If you are present at departure the ATC cue will seperate them at take off. But....if the flights are spawned enroute (at the time you start the sim or they fly into your active ai area), they will be in tandem.
You would need to edit the times in one of the flight plans.
Dave