On June 7, 2004, at about 0732 EDT, a Virgin Atlantic Airbus A340-311, G-VFLY, operating as a 14CFR Part 129 scheduled passenger flight from Washington-Dulles International Airport (IAD) to London Heathrow International Airport (LHR), was mis-loaded at IAD. The captain noticed an unusually rapid rotation at IAD, but continued the takeoff. Enroute, the crew received two Fuel Excess Aft CG warnings, about 10 minutes apart, 2-1/2 hours into the flight. The gross weight CG indication was 34.0 and 34.2, respectively. He transferred all of the "trim tank" fuel forward, isolated the trim tank, and continued to LHR. Interviews with key ground personnel revealed that approximately seven tons of baggage was loaded in the aft cargo hold (positions 32-42) instead of the forward cargo hold (positions 23-26) as depicted on the load plan. There were 203 passengers, 12 cabin attendants, 2 flight crew, and 1 additional crewmember on board. There were no injuries and the airplane was not damaged.