When using the Internet Explorer based HTML to PDF option (the default in pre 8.3 releases, from 8.3 onwards the Print CSS media type is enabled by default), the PDF Converter does not go through Internet Explorer's print processing engine, so any print specific CSS entries are not used. If you have control over the page that is being converted then you can add some logic inside the page that looks at a query string parameter ( e.g. ?pdfconversion=true). Based on this parameter being present you can then emit different CSS / HTML that improves the formatting, e.g. a different page width. In SharePoint this can be achieved by modifying the master page or inserting a hidden 'content editor web part'.
PDF Conversion starts the moment a page 'finishes loading'. This generally works well, but some modern web pages rely on JavaScript to render part (or all) of the page. There is no way for our software to detect when the JavaScript has finished executing, as a result the converted PDF may only show partial information. As a workaround consider specifying a 'ConversionDelay' in our configuration file. Start with a high value (e.g. 30000 = 30 seconds) and if that works lower it to a more reasonable figure, often it just requires a value of 1000 (1 second)