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I've just started using the iCal synchronisation feature, and also noticed a few duplicate entries appearing. I do not sync iCal with any other software/device, and all OF synching happens within discrete calendars designated for the purpose (i.e. no non-OF entries in there). The duplicates I've encountered have all the same details, except that the OF reference URLs are different.

I just tried modifying a detail on one entry, and it synched ok, transferring the change through to one of the existing entries, but left the duplicate in place.

The only non-standard use recently is the transition from Leopard to Snow Leopard, for which I did a clean install (i.e. not using Migration Assistant), and copied across the Preferences file and Application Support folder, then upgraded the OmniFocus software when prompted that I didn't have the latest version. I notice that this newer version mentions updates to sync issues in the release notes.

OmniFocus 1.7.3 (v77.40 r118571) running on Snow Leopard (10.6.1).