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On importing existing users, these won't get updated but are added instead.
This happens, if the import-template was generated with version 6.x-4.2 which lacks the option "import_key". Having such a template, the code in user_import.import.inc line 17 initializes $import_key with "user-mail". On the other occurrences of $import_key the variable is tested against "user-email", especially in line 89, which causes the wrong behavior.
Workaround: Creating a new template via Frontend initializes the import_key correctly.
Bugfix could be a change to line 17.
Sincerly
Michael