OmniGraffle 3.6 for iOS includes the same layout changes introduced in the recently-released OmniGraffle 7.8 for Mac.
OmniGraffle’s orthogonal line routing algorithms have been dramatically improved, as in the Mac version, making your diagrams even easier to follow.
And, from the release notes:
The new “Connected Objects” option in the Diagram Layout inspector allows you to use the Layout Now option without accidentally moving content that isn’t connected by lines in your diagram (like a header, footer, or logo).
Sample documents and templates have been updated to use the new option and the new line routing changes.