When the pilot of VH-SWT requested start approval and clearance at 0535 EST, the callsign was not that which had been flight planned. Processing of the new callsign and the allocation of a transponder code, along with other arrivals and departures, delayed the departure of SWT for about 20 minutes. The aircraft was to depart from runway 01 at the taxiway A7 intersection. At 0557, at B747 aircraft landed on runway 19. At this time, the high intensity runway edge lights, as well as the runway centreline lighting, were selected for runway 19. The B747 was still on the runway but south of the A7 intersection when SWT was cleared to line up. Because of this, the runway 19 high intensity edge lights were left on as were the runway 19 centreline lights. (The high intensity edge lighting and the centreline lighting cannot be selected for both runway 01 and runway 19 at the same time.) This meant that the only runway lighting iluminated for runway 01 was the white omnidirectional runway edge lighting. The green taxiway centreline lights were on. These extended from taxiway A7 to the runway 01 centreline. When SWT was issued with a transponder code and cleared for an immediate departure, the aircraft was at the holding point at A7. The pilot read back the incorrect code and was again given the correct code. To enter the code into the transponder, he had to lean across the cockpit to the right side of the instrument panel. He did this as the aircraft entered the runway. When he looked forward again, he saw a line of white lights directly ahead and commenced the takeoff roll. Almost immediately, he heard a noise from the left side of the aircraft and rejected the takeoff. The left propeller had struck one of the high intensity runway edge lights. The propeller was damaged and the light housing destroyed. It appears that when the pilot leaned across the cockpit to enter the transponder code, he veered left of the taxiway lights leading to the runway centreline and then assumed that the omnidirectional edge lighting depicted the runway centreline. As a result of this incident, Airservices Australia has written to the airport operator proposing that the lighting system be modified so that the centreline lights for runways 01 and 19 are omni-directional. A letter supporting this proposal has been sent from BASI Brisbane Field Office to Brisbane Airport Corporation Limited. The operator is issuing a memo to all pilots advising them of the incident and the runway lighting arrangements which can apply when one runway is being used for arrivals and the other for departures.