The ship in question is the Riftborn Wraith, using 3 H-Field Fleet Accelerators.  This can be seen the the attached "Slow ships.zip." Slow ships.zip

In trying to look at this a little further, some other odd things happened.  I moved my fleets and reorganized them.  I now have 2 Wraiths and 1 Spirit class ships in the fleet for a total of +6 speed to the fleet).  Oddly enough, the fleet has a total of +3 to every ship.  These changes can be seen in the attached "Odd changes.zip." Odd changes.zip

Additionally, the other nearby fleet with my hero in that save is seeing some odd things too.  The ships in that fleet have -5 speed from what they should be.  I'm guessing it's related to the Lunchtime event, which should only decrease speed by 2.

I will point out that these mods also cost double the declared value to put on the ships.  I know this is normal as you are in truth adding 2 modules to the same slot on this type ship.  However, like all speed related modules, you still only get the benefit once.  Just mentioning it again since it doesn't make sense with the rest ship design.

As for the problem with completing the quest, I was able to get through it from your suggestion.  I originally had my hero in his own fleet.  I tried combining him with other fleets many times, but this time unassigned him and then directly assigned him to a fleet instead.  This completed the quest instantly.