It's like I said it before; the 0 byte thing is when it doesn't restart your phone properly.
So I install new shiny PCSuite (reboot), plug in my phone, go to backup manager.
Click on backup, and it first creates the 0 byte problem, and you'll notice the attempt for PCSync to restart your phone basically 'times out' (the icon spins and spins, it doesn't shut down, and then it gives up).
At this point, completely shut down your phone, start it back up again. You'll enter your PIN as normal.
Now repeat the attempt to backup again, this time the phone restart window's progress icon doesn't spin round and round, it stops for 30 secs, and then the phone restarts itself without assistance.
When it comes back up again, you aren't required to enter any PIN (you can just slide-unlock if you wish), and then a different notification window pops up on the phone saying that the backup is in progress, and it finishes what it set out to do on the PC side.
New folder is created in my backup location with data in it, the byte count up the top is the amount it reports (on disk though, it's only about 24MB).
When it works, it does only take a couple of minutes.