But it is rebuilding the database everytime I reboot.

Those steps (if followed precisely, especially/specifically the EXIT command) are supposed to rebuild the database and fix the problem, thus making it so that you don't have to do a synch.

The part of the synch that fixes the database is where it runs the player software with the drives read-write. Should be the same thing.

What is happening when you hit that command? Can you send us a serial log of exactly what you're typing and what's coming back out?