Dinger
The flight crew disregarded the message, because they assumed that the Calculated quantity was the FMS' version of the planned fuel remaining quantity, based on predicted performance according to what planned engine settings were and the aircraft's route.)
The fuel disagree/leak checklists for the 777 are quite explicit that "calculated" for fault finding/QRH purposes is the instantaneous calculated on board fuel ( i.e. initial onload minus the integrated flow), and that is the number to be compared with the FQIS tanks totaliser figure; both are displayed for easy comparison, right next to each other, on FMS page Progress 2 (in our case). Since they are instantaneous, not predicted figures, there's no need for any future performance input/knowledge of route, etc.
On most flights the two figures will be well within a within a tonne of each other. Now from the report it seems the SIN crew had a 4 tonne mismatch (!!!!) so unfortunately it looks like they well and truely managed to over analyse things and talked themselves out of actioning the Fuel Leak checklist...however...
Don't want to offend tdracer or Boeing but you mention the comment in the report about the training of the fuel disagree/fuel leak checklist, and I'd say that could well be a fair cop.......FWIW for the 777 this has been a very "hot" item for trainers for a while at at least one outfit I know of. The checklists are somewhat protracted (for good reason), convoluted, but there are one or two interestingly worded questions and as a result using the electronic checklist it is quite easy to end up ticking the wrong box and going up a blind or misleading alley, or not going up an alley at all (such as going into the Fuel imbalance Checklist but then not going on to action the Fuel Leak Checklist....when in fact taking a step back it might be obvious it is the sensible thing to do).....
Does the FMC use Calculated fuel as the basis for its Arrival Fuel Prediction?)
FWIW Arrival fuel prediction (FMS progress page 1) does use the calculated fuel minus predicted burn, winds, temps etc etc. There is an option, rarely used to switch to using the FQIS quantity..but in any event you shouldn't be using that predicted figure arrival as a decider for Fuel leak analysis, it's the instantaneous calculated fuel vs. gauged fuel tanks that matters..