Backups now back to normal.
I have a main computer which I store all my data a G5 iMac and a Hackintosh netbook. I backed up overnight onto the Hackintosh then did a restore on the iMac. selected "do not backup" and the restore took about 15 mins till the point at which it asks if you want to restore from a backup. the last backup was on the 17th June, which is when I install OS 3 onto the ipod so I did not restore.I put the ipod onto the Hackintosh and restored from the overnight backup, this put back data for emails but only the bare minimum programs and no music, so I discovered that the backup is only data and not media or program files. I then put the ipod back on the iMac and synced. Again the backup was taking a long while so i cancelled the backup and the sync continued and put my ipod back to how it was before I started, Phew!. Now thanks to Pete for the tip about forcing a backup, I backed up the ipod. it took 1 hour and 9 minutes, the progress bar only move about 1/4 of the way for the 1st hour and then finished in a 9 minute spurt. Now the good part, a backup now only takes about a minute. I kept changing a calendar on the ipod and syncing it with iCal, this caused a backup before the syncing.
Conclusions, well I think that Pete was right that OS 3 did not auto backup and so the backup was so out of date that there was a lot to backup which is why it took so long. Now the backup is up to date and it seems to autobackup before syncing, the backups are very quick.