Rage and ODL
The 744 flaps 5 to 1 selection would almost certainly generate significant aerodynamic changes since it combines the largest area change with a removal of approx one third of the leading edge devices.
The 'no jettison with flaps between 1 and 5' rule is due to the juxtaposition of the jettison nozzles and the outboard L E devices. The vortex generation pattern will change markedly during that particular range of flap deployment/retraction.