I'm so sorry, I'm really flummoxed by this.
The only thing I can imagine is that it has something to do with how you made the blank document, right back at the beginning.
Can you test it for me? Make a new blank file at exactly the dimensions you require (at 300ppi, I figure). Scribble on it with the brush tool, or something, then save it as a pdf, then open that pdf in Reader and see what the size is.