I'm sorry for the confusion this is causing - are you having trouble with the PDF of our printed manual, or with the help menu content?
If the latter, it sounds like you have multiple copies of OmniGraffle installed on your machine. Unfortunately, the built-in help viewer gets confused fairly easily, which results in (for example) the OmniGraffle 4 help being displayed in OmniGraffle 5. That sort of sounds like what's happening to you.
If it is, this page will show you how to correct the problem:
http://www.thexlab.com/faqs/helpviewer.html
Does that help? Again, very sorry for the confusion this caused.