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I also submitted this officially to omnisupport, but wanted to see if anyone else has seen this issue and/or has a fix:

I have an interesting syncing problem with iphone and desktop versions that keeps coming up even if I stop syncing and rest everything. I keep ending up with two "Miscellaneous folders" This causes a problem because the old one has all of my misc stuff and the new one is blank. Then, anything I check completed on the desktop goes into the new miscellaneous folder. When I move those item to the correct folder and delete the additional folder, it is recreated at next sync.

Also, but miscellaneous folders show up on the iphone version too.

Any thoughts on how to fix this one?

I'm not sure what you have is a synching problem.

I only have the iPhone version of OmniFocus. I do not sync at all but I too have a problem with the creation of multiple Miscellaneous folders. The extra folder is obviously created when I create tasks but other than that I have been unable to discover a specific pattern.

You might want to consider looking for somewhere other than the sync function for a solution to your issue.
Thanks for the feedback. I will keep an eye on that. Maybe it is just a bug in the iphone version and then the extra misc folder just syncs to the desktop as it should.
I, too, drag around two Misceallaneous folders with me the whole time, even though I've deleted one of them on occasion. I don't know whether it's a synchronization problem or not.
Well, I've gotten the multiple Miscellaneous folders bit with syncing between two desktop machines, with no iPhone involved. It is possible there is more than one bug here, of course.

At least on the desktop, the program will create a Miscellaneous folder for you if you have the right settings in your preferences. It does this when you have an action in the Inbox with just a context assigned, your clean-up preference says it is okay to clean up items as long as they have at least a context assignment, and the default list for single actions isn't set to something else. Some of these settings (possibly all, I'm not sure) are synced over to the iPhone.

If you do get the multiple Miscellaneous folders, moving all the items into the correct/original folder, deleting the usurper(s), then setting the default single action list to the correct/original folder again (in that order) should get things squared away. I would do an immediate sync at that point.
I have this problem, too, and was just about to post. I delete it, then a couple of days later the misc. folder magically procreates! When I delete the new one, it always tells me there is a hidden file that will also be deleted.
I have the same problem as well.
Maybe OF is telling us we have way too many miscellaneous items??? ;)
I have found that when you do delete the second Misc folder, make sure to view all items perspective first and make sure to move those items out if you want to keep them.
same here, always have 2, have deleted them in the past but they come back on the next SYnc

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