I loaded the updated plugin onto a freshly wiped test server and here are some of the default values I'm getting in the data file. Not all, but a lot of the stack sizes are not what they should be. Config file hasn't been changed.

"ItemId": -1018587433,
"Shortname": "fat.animal",
"HasDurability": false,
"VanillaStackSize": 10000000,
"CustomStackSize": 10000000
},
{
"ItemId": 609049394,
"Shortname": "battery.small",
"HasDurability": false,
"VanillaStackSize": 10000,
"CustomStackSize": 10000
},
{
"ItemId": 1719978075,
"Shortname": "bone.fragments",
"HasDurability": false,
"VanillaStackSize": 10000000,
"CustomStackSize": 10000000
},
{
"ItemId": 634478325,
"Shortname": "cctv.camera",
"HasDurability": false,
"VanillaStackSize": 640000,
"CustomStackSize": 640000
},

Unload StackSizeController, delete data file and config file, load StackSizeController.

If you have any plugins that affect stacks, also unload them first.

Thank you, today's update has sorted out the issues I was having.