Take a look at this recent similar thread:
How to stop application folder form disappearing from the dock
I don't really understand why the solution given there worked, whereas just disabling the Dock syncing didn't, and I also don't understand the role of iSync.app, since I believe this app is no longer used for computer-computer syncing.
Take a look also at this Apple support article:
MobileMe: How to reset sync data
I don't know if this does the same thing as the iSync procedure.
Anyway, you might try the iSync method first, since it worked in the other thread. Some additional Googling first might be helpful. Be sure everything is backed up in any event.