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If you turn on Reminders Capture in OmniFocus, it will move reminders from the Reminders app to your OmniFocus Inbox—which is a great way to add tasks to OmniFocus using Siri. (We don't leave the reminders in both places because you'd get multiple reminders for them and have to check them off twice.)

If you don't want this, you can either turn off the Reminders Capture feature—or you can create a separate list in Reminders and tell OmniFocus to capture from that list (leaving all your other Reminders lists alone). On iOS 6, you can choose which list you'd like OmniFocus to capture from. (This choice appears when you have more than one Reminders list.) On iOS 5, the alternate list must be called "OmniFocus".

Hope this helps!