Microsoft’s Remote Desktop Protocol has a flaw when printing PDF documents with embedded fonts, where the fonts are not passed to the Print Spooler. The same document will print fine from the Server’s console.
The currently solution for this issue is to print the document as an image.
From the Adobe Reader, File > Print dialog box, click on the Advanced button and make sure that the Print As Image box is checked.
The document can then be printed normally and the PDF will print correctly. This will result in slower printing as you will be spooling very large image files to the printer, but you can speed this up by printing the document at a lower DPI such as 300 DPI.