While they were still sitting on the plane at the gate at IAD, the flight deck crew told passengers the delay was due to their request for a software update for one of the engines, which the crew described as running faster and unable to sync with the other engines.
As others have noted, they didn't give you the whole story - or quite likely any of it. The Engine Controls (FADECs) on the 747-400 are
not on-wing software loadable. To change the FADEC software, the box needs to be removed and replaced (software loading is only done in a shop environment and requires the box be literally opened up, after which a pass-off functional test is mandatory).
Educated guess, there was an existing engine control fault that they dispatched with via the MEL (FADECs are redundant, fault-tolerant system and time-limited dispatch is allowed for loss of redundancy faults). However if another fault occurs it can put the engine control into a no-dispatch state and maintenance action is mandatory.
Futhermore, since we're talking Rolls Royce, the engines really are not "FADEC" - rather the RB211-524G/H on the 747-400 has a "Full Authority Fuel Control" - FAFC - unlike FADEC it doesn't control the inlet guide vanes or bleed valves. The vanes and bleeds are controlled by a fluidic mechanical control system - no electrons involved.
It's quite possible since they specifically mentioned 'running faster' that the fluidic vane controller went south and needed to be replaced to prevent an N2 overspeed issue (the fluidic vane controller has been rather problematic in service).