Yeah, the unprocessed "natural" stuff will separate; I have a jar in the cupboard and keep it on its lid so the oil will be on the bottom. The "name brand" ones like Jif, Peterpan etc, have added ingredients which stabilize the peanut butter so it will not separate, not to mention sugars, salt, etc.
The powdered stuff also contains salt and sugar, but I believe the oils have been removed. So I'd probably use the powdered stuff.
Insert catchy signature here....