Hello everyone,
I also have the iCloud bookmarks sync problem on 3 devices : iMac (27” late 2009 10.8.4) + iPhone 4 (6.1.3) + iPad 1 (5.1.1). My Safari bookmarks.plist file on the Mac, full of duplicated bookmarks, was up to 18 MB!!! So I was experiencing many freezes / unexpected quits while browsing, making Safari unusable. It was even worst on the iPhone/iPad where Safari was quiting on launch.
I finally unchecked the Safari bookmarks sync on iPhone/iPad and cleaned up the 25.000+ “NO_TITLE” or duplicated bookmarks on my Mac directly in Safari (not by editing the bookmarks.plist file manually witch didn't work for me). Bookmarks are now clean on the Mac and in iCloud.
The problem remains with the iPhone/iPad : if I reactivate the Safari bookmarks sync on iPhone/iPad, the old 18 MB bookmarks are coming back to iCloud from the iPhone/iPad. In fact, the old bookmarks are still on the iPhone/iPad, even if I've deleted them before (when I unchecked the bookmarks sync over iCloud)!
In Safari iPhone/iPad, there is no bookmark when I click on the bookmark icon (witch is good because I've deleted them). But when I try to create a new bookmark for a webpage, I can see the old bookmark folders are still there when I navigate to select the location where to save the bookmark. So if I reactivate the bookmark sync for the iPhone/iPad, the 18 MB bad bookmarks are coming back to iCloud (merge)!
Can anyone confirm that the bookmarks are not really erased when unchecking the iCloud bookmark sync, and if they are still visible when saving a new bookmark on iPhone/iPad?
Except erasing completely the iPhone/iPad system without restoring from a backup (empty iPhone/iPad = bummer), I think the solution to get rid of those "ghost" bookmarks would be to delete the Bookmarks.plist files directly on the iPhone/iPad, or at least in the iPhone/iPad backup files located on the Mac (and then restore the iPhone/iPad from this “cleaned up” backup). But the file structure of the backups is not so “human-friendly” and I don't now how to locate the right file to edit/delete.