The change in font size is probably because of the way Manager’s PDF service creates randomly named fonts on the fly (see Save as PDF using Manager's internal PDF driver?). When you open the PDF file later, it cannot find the random font that is specified in the file, so it substitutes a local font that has similar appearance. Unfortunately, in your case, the local font is sized differently, so it throws off your alignment.
In addition to doing what Lubos recommended, you can make sure that you enable the option in your PDF driver to embed all fonts. (Also make sure you disable the option in your PDF viewer to use local fonts.) This will make the resulting file much larger, though, so you may or may not want to do it.