on our 777, the clocks are usually set to UTC (displays AIMS generated UTC time and date which comes from GPS). however, they can be set to MAN (if so required).
what is more interesting is how the FMC uses the time for ETO? boeing's FMC always round-down the time to the nearest minute i.e. 22:34.9 =>22:34. 'Apparently', it isnt so on the airbuses (can someone confirm!).