Interesting, I’ve been having the same issue here with my Canon MF216n printer. It will not print properly. Includes edits made in apps like PDF Pen. The same PDF’s will print fine on my HP printer. Something seems to be going on with Canon printers. 
Are you seeing blank pages printing too?
Update: Canon Customer Service & Support informed me today that my inquiry was forwarded internally to their Product Specialists.
Nice! Thanks for the follow-up.
/fingers crossed 
No, my issue is that certain “objects” or things I edit on the PDF on my Mac do not show up when printed to the Canon, whereas they print fine to my HP printer.
I would discuss this with Canon.
Update: After quite a while German Canon Services & Support informed me today that the only solution they can offer is to use Adobe Acrobat Reader to print PDFs properly on the Canon printer. This actually does work on my setup. My standard PDF Tools (DevonThink, PDF Expert, Apple Mac Preview) still do not work. (And Adobe Acrobat Reader is no option for me for other reasons.)
Canon Support did not even reacted to my clear statement, that all of my PDFs print just fine with all of my mentioned PDF Tools when printing to an alternative printer (Samsung). This pretty clearly makes this look like a Canon issues to me.
For my case, Canon does not want to do more than suggesting a workaround unfortunately. 
Thanks for the follow-up. It’s appreciated despite the response you got.
Wow thanks for posting this Tim. It would have taken me a while to narrow the issue down to the printer. Same problem here - unfortunately trying to contact Canon support is rather a pain (only phone support 7 hours a day).
Could this be an issue with the way ABBYY creates the PDF? I have to say that I’ve never had blank pages on my Canon with other applications. It’s crazy frustrating to think you’ve printed something out only to later find a whole bunch of blank pages at the printer.
Note what he said in his post…
Right, so my understanding of the issue Tim had (which, if correct, matches the issue I have):
- Only PDFs created by ABBYY OCR (aka by DevonThink) are affected
- The issue happens on most PDF viewers (apart from Adobe - I haven’t tried Adobe, I don’t have it installed)
- The issue only happens on Canon printers (Canon MF8050Cn in Tim’s case, imageCLASS MF634Cdw in mine)
If Canon isn’t willing to look into the issue, perhaps digging into what ABBYY OCR is doing differently in the PDF creation process is worth looking into?