They seem to have updated the way ark does PGMs, and it's no longer the settings in the ini.
Create a local Ark, go into the map locally and then back out. From there you will find the following file in something like (depending on where steam is installed on your machine):
C:\Program Files (x86)\Steam\steamapps\common\ARK\ShooterGame\Saved\SavedArksLocal\MySavedPGM\MySavedPGM_v2.ark
copy that file to the server, except instead of the directory 'SavedLocalArks\MySavedPGM\' it'll be something like 'SavedArks1234\PGArks\PGARK' folder, so...
{FTP Server}\Saved\SavedArks1234\PGArks\PGARK\
then remove all the previous PGMap data from your game.ini file and just put the map name, for example:
[/Script/ShooterGame.ShooterGameMode]
PGMapName=MySavedPGM
OverrideOfficialDifficulty=5.0
etc.