Hi,
Please try the following:
1. Try to update to the latest build and see if it fixes the problem. We have done many optimizations over the years so the latest may work better.
2. Check your web server logs. It's possible that your server simply refuse to serve all the contents when its load is high. In that case obviously you won't get all the output in the PDF file. If you use ConvertHtml, you will want to log the HTML you passed to the converter, then compare the logs between "good PDF" and "bad PDF" and see if you can find anything difference between the input;
3. Try to increase HtmlToPdf.Options.MinLoadWaitTime. If your page uses AJAX to load additional contents, then it's possible that the converter will start converting before your AJAX code has finished because the converter does not know when your code has finished loading contents dynamically. If that's the case, you can also consider manual trigger:
http://www.essentialobjects.com/doc/4/htmltopdf/eo_js.aspx#manual_triggerHope this helps. Please let us know if the problem continues.
Thanks!