Which version of ColdFusion are you using? (It may not actually matter.)
My clients noticed this and many other rendering issues when using CFDocument, so we experimented with generating HTML files (using CSS with absolute positioning, SVG images, WebFonts, etc) and then used the free command-line program WKHTMLTOPDF to convert it to a PDF. Using this method, we were even able to add HTML to headers & footers. We could also force sections to stay together by using CSS "page-break-inside:avoid". In addition to looking better, generation time was faster (or could be offloaded in the background without using a CFThread) and the file sizes were smaller.
Generating PDFs using ColdFusion & WKHTMLTOPDF
So, use a smarter tool. Interesting. Thanks for the blog link
It's been the best decision for us as it provides consistent quality irregardless of which version of ColdFusion we are using. I can also use a scheduler and batch process static HTML files in the background without having to use ColdFusion. (The EXE files appear to be portable too.) It uses a headless WebKit browser to render the pages... so if it looks good i Chrome, your PDF will look good too.
You can test WKHTMLTOPDF by downloading it to your PC and then running the simple command line to convert any webpage to a PDF:
wkhtmltopdf http://google.com google.pdf
NOTE: Use "WKHTMLTOImage" to save the webpage as an image.
From there, you can experiment and add many other parameters to customize/optimize the PDF that CFDocument doesn't provide.