The pilot of VH-MGW requested taxi clearance for take-off and reported in receipt of automatic terminal information service (ATIS) "Echo". The runway nominated by the ATIS was runway 35. The aircraft was cleared to taxi, but shortly after, the pilot requested runway 30 for departure. The Surface Movement Controller (SMC) then issued the following instruction:- "Mike Golf Whisky taxi for change of runway 30, hold short of runway 35." A Boeing 737 VH-CZD had been cleared to land on runway 35 and was beginning to flare for landing. VH-MGW was then observed to cross the holding point for runway 35. After repeated calls from the SMC the pilot of VH-MGW finally stopped his aircraft close to the edge of the flight strip. The Boeing was not instructed to go-around as it was at the point of touchdown and considered by ATC to be committed to landing. The pilot of VH-MGW stated he did not see the holding point markings until he had been instructed to stop by the SMC. He said the holding point markings had been changed and was planning to stop at the "old" holding point position. He also stated that he was aware of the landing Boeing 737.