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I have the same issue.

Having read on this forum about the URL being used as a key value for the sync I have been monitoring the value of the field in my iCal ToDo's.

For me everything works fine until Mail.app (Snow Leopard) is started or restarted. For a short period of time all the ToDo's (when viewed in mail.app) are greyed out, I'm guessing while mail.app gets the latest ToDo's from iCal. While this takes place all the URL fields get updated, so a URL that was previously 'omnifocus:///task/fw0avcjKWJ6' gets changed to 'mailitem:818D81AE-D6C8-4543-A139-66CB06173256?type=todo&action=showparent'.

At this point I delete all the ToDo's in Mail.app and re-sync OF (ver 1.7.5) with iCal, and then the cycle repeats. :(

Is it possible to disable ToDo's in mail.app?