Sometimes when troubleshooting aspects of OS X, we resort to a routine of disabling features and removing configuration files to have them recreated freshly. While this is an approach that is sure to give you fresh configuration files and ensure that settings or configuration options are not contributing to the error at hand, sometimes it is not always necessary to do.
Recently as part of one of the MacFixIt Answers columns I offered a couple of suggestions for fixing Safari bookmarks being duplicated when synced with Apple's iCloud service. One of my suggestions was to remove Safari's bookmarks property list file; however, a slightly alternative approach which MacFixIt reader "rkaufmann" applied might work better in some cases.
Instead of clearing out the preferences file and having it be recreated, since this file is being updated to match that of other systems when synced with iCloud, rkaufmann found success in clearing synchronization problems by manually copying the file from one system to the other one, replacing the file.
I tried your solution [for fixing duplicated bookmarks,] however it did not work in my situation. I am running Lion 10.7.2 on a late 2010 MacBook Air and the same version of Lion on my late 2007 iMac. The problem was with my MacBook Air...because Safari was performing perfectly on the iMac I simply copied the iMac's /username/Library/Safari/Bookmarks.plist file to the same location on the MacBook Air, and then turned on Bookmarks in iCloud Preferences on the MBA and my problem was fixed.
It took me a little while to figure it out but so far it's been stable for about 6-7 hours.
If your system is experiencing errors that you suspect might be rooted in a configuration file, especially if the file is one that is shared or synchronized with another system, then you may benefit from performing a manual synchronization such as this. When the system automatically synchronizes it will perform checksum routines, date checks, and other options to determine which file was updated and with what new content. Errors in the file that affect these routines can result in improper or broken syncrhonization, and manually copying them will sync them up again.
Even if files are not synced, such as the preferences for programs like Pages, Preview, or TextEdit, you can sometimes have success in fixing odd program behavior without resetting all program settings by copying the preferences file from another system that you use.