There is a common error that comes up when people print our PDF's; when you have a letter size or 11x17 pdf that would print true, there is an option to reduce to printer margins. This happens at printing the PDF, not when it is created. Acrobats default print setting is set to scale to margins, but page scaling needs to be none, when you print.
Perhaps you know this, as in your post you say you are careful on the pdf settings, but maybe you are referring to when you making them, not to the printing side?