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OmniFocus backups are package files directories full of many other files, masquerading as a single file. Select one of your backups, right-click and choose Show Package Contents and report back how many files are in one of your backups. Just about any copying of a package file with lots of internal files will take appreciably longer than a plain file occupying the same number of bytes on the disk. If you do not sync OmniFocus, the database backups will probably have many, many files (roughly one per change made), and occasionally using File->Compact Database should make future backups less tedious to handle.