Is the PDF paper size the same as your printer paper size? In Adobe Reader, you can check with the Document Properties, or mouse over the lower left corner of the window to check.
Does the PDF get scaled when you print it out on paper, or is it printed at its original size? Check your PDF viewer's print dialog for that one.
When you check the margins with an on-screen PDF, did you set the viewer's zoom level such that the width of the PDF on-screen is identical to the width of your paper size? For example, on some of our screens, a zoom of 82% results in an 8.5 inch wide page on screen, and then we can use a ruler to gauge if margins or other measurements are correct. If the zoom level is different, the ruler measurements have to be scaled accordingly.
For the larger error, you're probably failing to account for the height of a page header in addition to the regular margin.