When you made the change, did you click save? If someone didnt save, and server reboots the stack setting is not saved.
You may want to also try a rollback from your recovery backups and see if that work.
Feel free to contact Nitrado Support to further investigate.
Link: Support | nitrado.net
My server running only for steam and map genesis, and in my game.ini i have setting some item stack to 250. And In this morning, items not setting in game.ini have stack 1 instead of 100 normal. I dont using ultra stack mod or any mod relate. Just fix some item in game.ini. Please help me!