I use SyncTogether to keep my iMac and MacBook (both Leopard) in sync. I usually sync iCal, Address Book, bookmarks, notes and Dock items. Several days ago, however, I started to notice a very annoying issue with my iMac's Dock: some items started to move around on the Dock, or completely disappeared from it. Even if I placed the vanished items back on the Dock and selected Keep in Dock, they vanished after a while.
I can't remember what was I doing when it started, but yesterday, the problem replicated itself to the MacBook. Other accounts were working normally, but not mine. I deleted the com.apple.dock.* files, but nothing changed. After using fsevent for a while, I noted some recent activities in ~/Library » Application Support » SyncServices » Local.
I decided to make a backup of that whole directory, and in a brute force way, I then deleted the content of the clientdata and DataReferences folders within that directory. After setting up my Docks again on both machines, everything has remained in place -- so far, the Dock is working perfectly on both Macs.
I'm not positive if this is related to SyncTogether, but I mention it because the solution was related to syncing. I think I synced Preferences, too, one time not so long ago, so maybe that was the origin of all these problems. In any event, I hope this helps someone who may be having the same issues.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20080509032108837