I generally keep the iTunes "Copy files to iTunes Music folder when adding to library" unchecked -- I prefer to organize my tunes by hand. When Syncopation sees this setting, it stores the copied files in its Application Support folder, which is what was happening during the sync. Flicking that option made everything work again. I'd prefer that this option not affect library synchronization and that the files go into the iTunes folder but it's not a barrier to the program's utility.
Compared to Tune Ranger, Syncopation worked far faster, which is to say hours rather than days depending on your library size. I didn't need to worry about file types either. I could choose to sync or not sync Movies, TV Shows and Podcasts via the Sync settings rather than having to figure out actual file extension types. What I could not do, however, was control iPhone application and iPod game sync, which is a needed feature for future releases.
The interface is functional rather than beautiful -- although beautiful is overrated when it comes to getting the job done. Although it's missing Windows support, I'd still give the overall Syncopation experience a solid B compared to Tune Ranger's C. There are still a number of synching apps that readers suggested I try out so the iTunes file transfer story isn't over yet.