Probably your game is using Init = Clear in the shiplist.txt file.

In PHost 4.0i and later, the PlanetsAttackKlingons, PlanetsAttackRebels, AllowOneEngineTowing, AllowCrystalTowCapture, and AllowPrivateerTowCapture options only describe the initial assignments of the PlanetImmunity, Tow and Boarding abilities, respectively. The same holds for the FullWeaponry part of AllowFedCombatBonus. Init = Clear will wipe out these assignments, so the Rebel/Klingon ships will not be immune, ships will not be able to tow and board.

There are two ways to solve this problem by changing the host configuration:

  • Switch to Init = Default. This will, however, also assign initial values to all the other abilities, so make sure you're not introducing unwanted abilities here.
  • Add the missing abilities to your shiplist.txt file. The following fragment adds the former racial abilities:
    AssignTo = Hull
    Function = PlanetImmunity
      Hull = *
      RacesAllowed = 4 10
    Function = Boarding
      Hull = *
      RacesAllowed = 5 7
    Function = FullWeaponry
      Hull = *
      RacesAllowed = 1
    Adding the Tow abilities is a little more work, you would have to list all ships that should be able to tow in your config file. The following fragment would work for the standard ship list with one-engine towing disabled (split into two statements for convenience):
    Function = Tow
      Hull = 3-8,12-14,17-23,25,26,28-50,52,53,55,56,58,60-64
      RacesAllowed = *
      Hull = 67-70,72,74-76,78-84,86,89,90,93,94,96-102,104,105
      RacesAllowed = *
    If you want all ships to be able to tow, it is of course enough to have one Hull = * line.