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Sync times can vary quite a bit depending on how much needs to be transferred and processed, and especially if database compaction takes place. I'll try to describe a set of repeatable measurements in the hopes of being able to compare apples with apples.

Start up OmniFocus on both desktop and iPhone/iPod. After both have started up and become fully active, click the sync button on desktop, wait for it to complete, click the sync button on the iPhone, wait for it to complete, and sync the desktop one more time. This should ensure that both devices are fully up to date with the central database and each other.

Add an action to the inbox on the desktop, click sync. My elapsed time for the sync wheel on the desktop (2 GHz Core 2 Duo MacBook, 2 GB RAM, 10.4.11, OF sneaky peek 1.6.1 (v77.16.4.0.112048)) to stop turning is about 2 seconds.

Now force the iPod to sync, and the elapsed time for its sync wheel to stop is about 5 seconds.

Add an action to the inbox on the iPod and force a sync. Elapsed time about 12 seconds.

Sync desktop to retrieve that change. Elapsed time about 3 seconds.

Now, launch a different application on the iPod. Go to desktop and individually enter 20 more actions in the inbox, syncing after adding each one.

Open OF on iPod. No sync takes place, despite Auto Sync being on. Opening time is 6 seconds. Force a sync to pull in the 20 newly added actions, sync time is 32 seconds.

On iPod, mark those 20 actions completed and sync. Sync takes about 13 seconds. Note that this isn't quite the same as what was done before, as this will go out as one multi-part change in the same file whereas the other will have a transaction file for each action.

At that point, I unregistered my other clients and forced the iPod to do another sync, which compacted the database from 267 files (as seen on the iDisk from the Finder) to 152 files, and took about 110 seconds. This would be very inconvenient to have happen on app startup when in a hurry to add a fleeting thought! In practice, it doesn't happen to me. What seems to happen is that the machine which hasn't been syncing for a day or two while I've been busy elsewhere adding, modifying and completing actions ends up being the one to do the compaction when it does finally sync, and the mobile client is never that machine. Or maybe I've just been lucky!

After that compaction, the next sync by the desktop (no changes to contribute) took about 10 seconds. After that, times seem to be back as they were before, repeating a few of the measurements.

I'd be interested to see the results if you try the same methodology. I'm suspicious that the long sync time you saw on the iPhone to add one item was perhaps doing more work than you realized.

I'm still wondering if differing software versions might be playing a role here, too. I've got OmniFocus 1.2.2 (v77.17.2.0.110617) on the iPod -- is that what you have on your iPhone? What about on the desktop?

Yet another question for me is why Auto-Sync doesn't seem to force a sync every time I launch OF on the iPod. I'm not complaining, just curious how it magically seems to know what (not) to do :) Does it always sync on startup for you?