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It sounds like you've fallen victim to some unfortunate terminology overlap.

There is MobileMe, Apple's "cloud" service, which offers as one of its components syncing of files stored on your "iDisk". MobileMe also offers WebDAV access to files stored on your "iDisk", and that's where the trouble starts. OmniFocus does network syncing of OmniFocus.ofocus via the WebDAV protocol, and MobileMe is one of the suggested providers of such service. However, if you have MobileMe set to sync files on your "iDisk", it does so via its own means, and has no understanding of the interrelationships between the many small files that make up the OmniFocus.ofocus "package" file (it looks like a file, but really, it is a directory full of files). Further adding to the trouble is that "iDisk" syncing happens after a delay; your Mac writes changes to files on the "iDisk" to a disk image on your disk, and only periodically sends those changes off to MobileMe (and gets changes from MobileMe that might have been made elsewhere). OmniFocus, on the other hand, writes out its changes to its database immediately via WebDAV. Couple that with the lack of understanding by the MobileMe sync software of how an OmniFocus database works, and it is just a matter of time before something breaks.

What to do? Well, I think you've already settled on the best solution for most people—use the Omni Sync Server instead. The errors you are getting now from MobileMe are complaints that it doesn't know how to reconcile the changes in the OmniFocus.ofocus file on your MobileMe "iDisk" storage, and they will continue until you remove the file. You are no longer using it, so that is what you should do. It is in the Documents folder in your "iDisk".

If you want to continue to use MobileMe to store your OmniFocus database, there are two options:

  1. Turn off MobileMe "iDisk" syncing
  2. Store your OmniFocus.ofocus database elsewhere on your MobileMe "iDisk"

Option 1 is done by going to the MobileMe preferences in System Preferences, the iDisk section, and clicking the button to turn off iDisk Sync. This means that you will no longer have access to files stored on your "iDisk" when your computer is not connected to the Internet. This is less likely to be an issue with a desktop machine, but might be for a portable. Personally, I've never found the MobileMe-provided file sync to be very reliable, and use Dropbox for such purposes now, with much better results. I guess the novelty of the MobileMe service wore off for Steve before he'd spurred the troops on to make it something really great.

Option 2 is done by configuring OmniFocus to use MobileMe sync (which to be clear, is WebDAV syncing using MobileMe as the storage) but instead of storing the database in the default location, instead storing it in the Backup folder of MobileMe, which is not synced by the MobileMe disk sync software. That eliminates the "too many cooks" problem, leaving only the application which understands how to manipulate OmniFocus databases properly (that would OmniFocus, of course) doing so. If this isn't a sufficient description of how to do it, that's probably an indication that the Omni Sync Server is the best way to go, or ask the Omni support ninjas for help in setting it up.