When using an import file containing only user objects and using "DistinguishedName" header, the migrated users are created in the target OU which was selected during the migration session, not in the OUs which were specified in the import file based on the "Distinguishedname" attribute.
Import files can be used to determine the target OU location only in the following scenarios:
1. Where OUs and users are migrated in the same session and "Migrate selected objects with their OUs to the selected target OU" option is specified. In such case migrated users target location will be determined based on their relative object-OU source location. For the explanation on how this can be acheived please refer to SOL47605:
"Is it possible to migrate Users and OUs with an Import File"
NOTE: For GUI way of doing this please refer to the following KB article SOL20404:
"How to properly migrate the OU structure from source to the target AD (Active Directory) using QMM (Quest Migration Manager) GUI interface."
2. If the objects already exist in the target domain and "Merge and move the objects to the new OU" option is specified - QMM will than merge into the objects residing anywhere in the target OU structure.
In all other cases migrated objects will be always created in the OU which was specified during the migration session regardless of the relative object-OU path contained in their "DistinguishedName" attribute.