[Brian]

I suspect this is just an issue of timing. We've observed that iOS tries to preserve battery life by shutting down wifi connections a little while after the phone goes idle - even if info is being sent. (This is not something OmniFocus is doing on purpose, in other words.)

Since OmniFocus' auto-sync behavior is also tied to the phone being idle, it's going to start closer to that "and now it's time to turn off WiFi" point. (Tapping the sync button resets the timer iOS is using to decide when to turn off the WiFi, so it gives you the maximum amount of time before that happens.)

We originally discovered this in iOS 3; it's possible that iOS 4 changed the behavior, but I haven't seen anything to suggest that it has.