First, the unread counter works with Apex Launcher, Nova Launcher, Smart Launcher 2 -- officially supported by each launcher's devloper.
Samsung's TouchWiz, Sony and their launcher, LG and their launcher -- not officially supported or documented by the respective manufacturers, intended for their own apps only, may work or may not work, nothing I can do.
But please check Aqua settings -> message notifications -> make sure that "launcher unread counter" is enabled.
PS - funny how there have been zero reports about LG or Sony, only Samsung...