I found that bulk import (in v1.1.3) duplicated accounts that already existed because we are appending the account suffix to the username, but it matches existing users based on the SAM account name only. To fix this I altered the code in bulkimport.php as follows:
$all_users[strtolower($user->user_login)] = $user->user_login;
becomes: $all_users[strtolower($user->meta_value)] = $user->user_login;
Then it seems to work as intended.