Please keep in mind that barcodes are printed by Aloha and not Punchh. If an older version of Aloha is being used at the store (e.g.: 14.1 or below), this issue will exist.
In order to ensure barcodes are printed in the center, upgrade to newer versions of Aloha (e.g 14.1 or 15.1). The alignment issues have been fixed in the newer versions.