I have fallen prey to the "ZFW as TOW" gotcha and had it picked up by the FO or relief crew. Not only embarrassing but quite shocking when you consider the implications.
That's why I brought up earlier that whoever is doing the calculations should have a gut feeling as to what the correct answer should be. Maybe these guys are flying too many types and can't remember what a reasonable answer should be. Did this crew fly this type plane to MEL? If so, they should have gotten something close to the same Vr that they got on that outbound leg. That in itself is a safety finding which should prompt a change in airline policy. Also, as previously discussed, some sort of acceleration check is certainly in order.