I have this issue too. Others (that I know) and all around the web have this issue, for a long time (several months it seems).
The error is bogus, as it clearly is capable of putting documents inside itself, but only when printed "to onenote".
I have read that this is a licensing issue between Adobe/Microsoft (although I don't understand why - pdf format is widely available in non-adobe products), and it makes no difference what version of pdf reader you use it seems. I have tried several, including
nitro, primo, cutepdf, and adobe, all of which fail.
This is a shortcoming of the Office software it seems, with no (known) solution, not a user configuration/installation error.