While creating a HALO script, I came across the same issue, and I posted here my findings.
While I don't know what your rappel script is doing in terms of code, I can surmise that it's the same thing: use the setPos command to move the unit out of the chopper *without* opening a parachute.
If that's what your code does, then that's wherein lies the problem. When you use setPos to move an AI unit out of a vehicle, the AI for that unit effectively ceases to function. The unit will probably fire back at enemies in range, but the unit will not move, nor will it follow the commands of the group leader.
Solution: none that I know of. Simply, you cannot use setPos to take a unit out of a vehicle.
Maybe you can force the unit to eject, which is safe to do, and then delete the parachute with deleteVehicle. E.g.:
deleteVehicle (vehicle unit1)
See if that works. Inject that into your rappel script.