Take off weight would have been in the range 340 - 360 tonnes, probably landing DXB a few tonnes under max landing weight.
Emirates system of cross checking entered performance data versus loadsheet data should have picked up any data entry errors. (ie ZFW as TOW etc etc) I always had a mental gross error check in my own mind as well.
I can't believe they would have used anything but the full length and 5 knots of tailwind would not have been a problem. Temperature was no issue.
If the above are eliminated as causes, it leaves rotation technique and shifting cargo . I've never had shifting cargo on an A345.
I can't imagine how, but if there was some very odd situation that involved incorrect performance data actually getting past the cross check, and then being used as the reference data for the take off ( ie low Vspeeds, low FLEX etc) it would be very interesting to see how the cross check system failed.