Could it be that the FM rounds up the minutes to the closest minute, up or down, while the ND simply display the minute regardless of the seconds?
For instance, if the eta is at 0612 and 40 secs, the FM will display 0613 and the ND will display 0612? Once the waypoint has sequenced, the actual minute is kept, so always rounded down (in this case, the FM would show 0612 for the last waypoint sequenced at 0612 and 40 sec).
