fred_the_red,
Taking off in a large jet, using balanced field length figures for every departure, is not the same as taking off in a light aircraft. At high gross weights all take-offs seem sluggish to start with. Then the acceleration picks up & you rotate with the end of the runway rushing towards you. Sometimes I wonder how we would ever stop from V1 in the runway remaining at that point, but you have to trust the figures.
If you look at the initial tailstrike location in the diagram in the accident preliminary report & allow for the 9 second time interval between initiating the rotate & first tail contact that is also in the report, the rotate position on the runway was about right for a normal take-off.
The extra 100 tonnes over the weight used for the calculations would have some effect on the time to reach rotate speed, but I don't think it would have been that significant. The big problem was that the speed attained was some 20kts short of what was required for the aircraft to fly at the weight it actually was.
The crew would have had very little indication that things were not right until they rotated & the aircraft did not fly. The aircraft 'always' flys when you rotate at Vr & the crew would have been wondering wtf was wrong. With the end of the runway rapidly approaching & not knowing what the problem was, the captain's first reaction was to command more pitch in an attempt to get the thing in the air. When that didn't work the only other option was to push the thrust right up & hope for the best.
When they finally staggered into the air I would be willing to bet that they still didn't know why the aircraft didn't want to fly at Vr. They may have thought of an incorrect flap setting, a screw up by the loaders & extra weight not accounted for in the figures or a number of other possibilities. It would have only been at some stage during this trouble shooting discussion that they would have realised what the problem was.
It is just extremely lucky that it was on 16 at Melbourne & they had the overrun & relatively obstacle free departure path that they had, or the result could have been vastly different.