I had a ton of firewall-related issues after Apple replaced the motherboard in my Macbook Pro; if the firewall is blocking the bonjour connection, that would explain what you're seeing.
(I kinda hope this isn't what's happening to you, because it was a pain to sort out.)
Easiest way to possibly resolve this:
Open the Security pane of System Preferences; switch to the firewall tab.
If the firewall is set something other than "Set access for specific applications", set it to that.
If OmniFocus doesn't appear in the list of apps below that setting, add it and set it to "Allow incoming connections".
Quit and restart OmniFocus on the Mac, then on the phone; does the sync work now?
If not, open up Console.app in the Utilities folder and enter "Firewall" into the search field in the toolbar. What appears in the window at this point? If you Open OmniFocus on your iPhone and try to sync, do new lines start appearing? If so, the firewall is blocking bonjour connections to OmniFocus even though you told it not to. (If no new lines are appearing, then the phone is just not able to connect to your computer; that's a different problem, but at least we've narrowed down what's going on.)
If you are seeing the firewall block Bonjour connections when it's been told not to, you'll want to print out
this page and head over to the genius bar. It's not exactly the problem you're having - it's a different networking technology - but the 'logic board swap causes firewall misbehavior' elements are the same.