[Brian]

Looks like this is unrelated to Safari 4, so I'm pulling my previous suggestion.

I tried the following before Safari 4 had been installed, with it installed, and after I removed it from my 10.5.6 machine. Worked as expected in all cases.

Open OmniFocus 1.6
make new action that starts and is due 2 minutes into the future.
wait for the appointed time to roll around - see "Available" and "Overdue" notifications pop up in Growl for that action.

So, let's try and figure out why something different is happening on your machine. What OS are you running? What builds of OmniFocus and Growl? Does anything that appears to be related appear in the console?

Console.app can be found in the utilities subfolder of your applications folder. Launch it, select "Open Console Log" under the File menu, and then press the "Clear" button on the toolbar. Once you've done that, launch OmniFocus, add an action like I described above, and wait for it to become available/overdue.

Paste anything that appears in the window during this process into an email, send it to in a response to the support ticket you opened, and we'll see if we can determine what's going on here.