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I had this problem last night after updating to, I think, 90500. I had it again tonight after updating to 90522. I may have messed things up extricating myself last night.

When OF re-opens after the update, I get a window with an error message. Tonight I'm getting two windows; they're both so long I can't see the bottom. There's no scroll bar, and the only way to get out is force quit.

The window starts with:

"Document has inconsistent transactions.

OmniFocus found inconsistencies between some of the transactions in your document. You can eliminate these by making a new backup and restoring from it.

Would you like to send details about this problem to the Omni Group? Your report will help us improve the future versions of OmniFocus.

Details:

F149AC57-7D1E-450B-B890-CFCF94D43C6C:0DFEAF18-C920-4C18-8C65-F53C05627694.xml (2007-08-28 04:53:13 -0500): hOhBet_YQa6: Update to nonexistent item (creating new item)
4AE4AE3B-6B13-4F15-B49B-B7D57CCF5D63:B817FC69-F44C-449E-AA6E-24A5E73B9421.xml (2007-08-28 20:17:18 -0500): o7YYWQXypDI: Update to nonexistent item (creating new item)
DB7C7456-4721-4F98-8170-6EC188DAEE3E:BE280623-25BC-4242-A4EA-22A62067BC84.xml (2007-08-28 20:19:17 -0500): lz-iOBNgPqc: Delete of nonexistent object (ignoring)"

And goes on and on.

Last night I had duplicates of all my projects and folders. I deleted the duplicates, which I think now was the wrong thing to do. I used OF a bit today without incident, and did a backup before I upgraded this evening.

But with those two windows with error messages, I can't follow the instructions to make a new backup and restore from it.

Any suggestions? The only thing I can think of is to make a safe copy of my recent backup, delete everything OF, and start over.

Thanks.