Thanks for your post.
This is probably because the release version of SQL Packager 6 always uses the 'include dependencies' option.
If you have any objects that have a dependency to a user, SQL Packager will always bring the deselected user back into the synchronization.
We have a patch release that enables you to turn off this option. Can you try it out and let me know if it helps or not?
ftp://support.red-gate.com/patches/SQL_ ... r91109.zip