The cause for the ETA discrepancy is most likely that a number of legs of the route have specific speeds configured instead of using the default speed.
In the waypoint list, any speed values shown in black are specific speeds set for that leg, while any speeds shown in gray are the default speed for the route.
You may right-click the speed cell in the waypoint list to quickly toggle between specific speed and default speed (the same goes for lane and turn).
The important thing to note is this: TECDIS makes use of the specific (black) speed for legs for ETA calculations in present speed mode.
In the extreme example with all legs with specific (black) speeds, present speed ETA is identical to planned speed ETA due to this behavior.
This allows you to set lower speeds as 'black' speeds on port approaches and departures, leaving other legs at the default speed. When calculating present speed ETA,
present speed is used for all the 'default' legs, but you get a more accurate ETA taking the slowdown during port approach into account.