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(Sorry I didn't notice this thread earlier; this is a repeat of what I posted on Friday over in the OmniFocus syncing forum)

OK, it turns out the problem isn't related to the 3GS, it's simply a bug with setting up syncing for the first time in OmniFocus 1.5 on iPhone OS 3.0. It doesn't happen all the time, but I was able to reproduce it in one out of three tries on my iPod touch.

The good news is that now that we've figured out how to reproduce the problem (at least once in a while), we've come up with a workaround (which we've also added to our FAQ):

I'm having trouble setting up Synchronization in OmniFocus for iPhone 1.5 under iPhone OS 3.0. Can you help?

There's currently a bug in OmniFocus for iPhone that may prevent you from successfully entering your credentials when syncing. To get around it when setting up synchronization:

On the first launch screen, choose "Make New Database" (counter-intuitive, right?)
Go to settings and set up sync as normal.
Go back to the home screen, and if sync is spinning without prompting for a username and password, quit OmniFocus.
Relaunch OmniFocus, press sync and you should be prompted for a username/password.