I had some uncheckable (fsck didn't find nothing wrong) error on the disk so i was unable to eject it.
After a very hard treatment with pdisk i was able to format the disk again, partition it and do a new backup.
I am able to eject now
Putting the destination partition on spotlight exclude list BEFORE the backup has resolved the other issue.
I understand that there isn't a way to resolve the program duplication problem.
How i can force super duper to eject the disk after the backup?
Thanks!