If memory serves, mission ships don't show up because they're not actually your ships, they're the private sector.  I'll verify that my memory is right.

If not blocked then the treasure Ship being private is the prob the private ships are not there.

If Paul is using a Civ from before the latest DLC/patch just editing the Civ and reselecting the ship set should solve his prob.

If they are blocked then he needs to use the Terrian ship set and Stardock needs to think about unblocking them.

Then if it's an pre-update Civ reselecting his ship set should work.

Was going to see if mine worked but just do not feel like playing 21 turns ATM.

Yes, I looked in my custom civilization and I did not have a "MissionShip".  I edited my custom civilization and, on the "Fleets" tab, changed my "Ship Style" from my custom style to the Altarian ship style.  I then saved my custom civilization.  After making this change, I now have the ability to successfully create "MissionShip"s.