iNotes makes heavy use of framesets, iframes and javascript, which is not supported by DominoPDF.
Therefore when using the URL interface of DominoPDF all URLs should have the &ui=webmail argument appended to the end.
The &ui=webmail argument tells iNotes to output content in the original Domino webmail UI and provides HTML / DominoPDF compatible output.
For example;
http://localhost/mail/prime.nsf/0/102CE45A2C0C92B5C12576790034301F/?OpenDocument&ui=webmail