Having the same issue as well, using the latest version.

as you can see the trader group has permission to enter, but in reallity they get blocked from entering the zone

    {
      "Name": "Alpha City",
      "Radius": 95.0,
      "Radiation": 0.0,
      "Comfort": 0.0,
      "Temperature": 0.0,
      "SafeZone": true,
      "Location": "-1225.479 23.64704 1132.308",
      "Size": "0 0 0",
      "Rotation": "0 0 0",
      "Id": "swamp_a",
      "ParentID": null,
      "EnterMessage": "You are now entering Alpha City, Base foundations that are larger than 4x4 are illegal! any part of the base that is outside that limit, will be destroyed",
      "LeaveMessage": "WARNING: Returning to PVP Area",
      "Permission": "trader",
      "EjectSpawns": null,
      "Enabled": true,
      "Flags": "Eject, PvpGod, UnDestr"
    },

EDIT* it actually creates permissions but if you are using a permission manager, it wont show up in it, hence you will have to assign them manually