Does anyone have any experience with synchronizing files across multiple machines at set times through VNC? Is there any software that can do this, looks like tightVNC is not capable of scheduling jobs ahead of time.
No. This is not an appropriate task for VNC. As Aaron stated you should use an appropriate tool for this. rsync and scp are commonly used and easy to schedule. If your are synchronizing configuration you should look at tools like puppy or cfengine.