When copying a list or library from SharePoint 2003 with its permissions, the membership of groups with custom permissions may differ from the source.
Due to differences in the way SharePoint 2003 handles group permissions, ShareGate Desktop is unable to migrate lists or libraries with groups that contain custom membership at the sub-site level : it will instead copy the group's membership at site collection level. Users that have been added to that core group will have to be re-added and given the correct permissions at the destination after the migration. However, all other permissions granted at the source are preserved.
In SharePoint 2003, it is possible to create a group in a site collection and then modify the members of that group on a per- sub-site basis. The concept of permission levels also does not exist in this version of SharePoint : the specific set of permissions are instead granted to the group. This has been changed starting SharePoint 2007 and it is now impossible to modify the members of a group at sub-site level, as the group's members are now defined at the site collection level only.
To try and bridge over this major behavioral difference between SharePoint 2003 and more recent versions, ShareGate Desktop creates a permission level with the same name as the group and the same permissions are granted to each member of the group at the site collection level. As it is impossible to redefine members for a specific sub-site, the members will be granted the permission level matching the group's permissions for every sub-site.
This issue occurs when ShareGate Desktop migrates a SP2003 list or library with permission granted to a group whose membership differs from its membership at the site collection level. To replicate the permission settings at the destination, ShareGate Desktop will break the inheritance and set the permissions to match the source which means the user permissions will be removed and a permission for the group will be added. However, new members of this sub-site won't be in the group and they won't have any permissions on the list.