Ah.. nice, i had to use IsoMaster instead to create an ISO which optimizes duplicate files.
The only thing i sometimes have trouble with is files which have the same name but different case, like "Backup" and "backup".
On linux this isn't a problem also the Rock Ridge ISO format supports this, but most of the time this isn't a real problem.
Would be nice if it were possible to rename or merge it just for the ISO creation, but that whould be hard to implement i think.