Certain mod-added items are doing the aforementioned annoying thing. So far I have noticed this happen to Banana (Faxpax) and Hamm's (ID). I updated ID earlier today. I have not, however, updated Faxpax for some time. The banana, upon consumption, produces a Banana Peel trap item. The Banana Peels produced by the separately-stacking bananas stacked normally. The affected items aren't appearing in my achievements window.
My mistake. Haven't updated Faxpax for some time either, though, so aside from changing a single word in parenthesis my report remains unchanged.
Also, only one of the stacks will be craftable, i.e. if I have a stack of 3 pear wines and a solitary pear wine I can only make one pear brandy. I think this means items are receiving weird metadata at random?