One thing I have meanwhile found out is that $isp_web->ptr_doctype_id is empty in writeconf.php
$ptr_dnss = $mod->db->queryAllRecords("SELECT dns_ptr.* FROM dns_nodes,dns_ptr WHERE dns_nodes.doc_id = \
dns_ptr.doc_id AND dns_nodes.doctype_id = '".$isp_web->ptr_doctype_id."' AND dns_ptr.status != ''");
i.e. the query returns nothing and make_named_reverse is not called.
However the doctype id (1033) in the DB dns_ptr is correct. Thus I do not know why $isp_web->ptr_doctype_id is empty in writeconf.php and not empty in lib/classes/ispconfig_bind.lib.php
EDIT: The doctype_id in DB dns_nodes is 0 for my folder "Reverse Delegation" which contains the PTR records in DNS Manager.