If stacking weapons with same durability and splitt them again, weapon has the ammo again.

Flamethrower fuel also. Wasnt this fixxed a while ago?

For me it works fine with no glitches. Try reinstalling StackSizeController server-wide, including configs, plugins, and even langs. If this doesn't solve the problem, there may be a compatibility issue with another plugin. If you provide a list of all plugins using the 'plugins' command in the server console, you can check compatibility based on the list provided by the developer.