I'm feeling a little dumb here. I've had some great, successful flights in the A380 but on two different occasions, I've run out of runway when doing flex takeoffs after the OIT told me it was no problem. Once was at Honolulu, flying to Tokyo and just yesterday it happened in Munich, flying to Boston. I waited until all PAX and fuel were on board, then ran the calculator and it gave me all my V speeds, flap settings, and flex temp. Then when taking off, I reached Vr about 500' past the end of the runway. As a test, I put the plane at Steward Field in New York that has a short, 6,000 foot runway where I knew I'd never be able to take off and sure enough, it gave me all the V speeds, Flaps 1+F and a flex temp. Isn't the calculator supposed to tell you that you need to use TOGA or "You can't do that. even with TOGA"? I feel like I'm missing a simple, important step but I'm not sure what that is.