You can't really tell if it's from the engine or not, until you shut down the engine. As Vilas illustrated, this isn't called for in your case, as the leak rate isn't high enough.
I would hazard a guess that it was a FQI problem. In A330/340 it's quite normal to have up to 700 kg less during some stage of the flight comparing fuel on board + fuel used with total fuel on departure.
Water in the tank can be one reason. Remaining fuel and fuelled fuel with different densities mixing slowly another.