We need to send out a separate IQ stanza for each affiliation

At least for Prosody.

src/converse-muc.js

@@ -605,9 +605,15 @@
                         onSuccess(null);
                         return;
                     }
-                    var iq = $iq({to: this.model.get('jid'), type: "set"})
+                    var room_jid = this.model.get('jid');
+                    var affiliations = _.uniq(_.pluck(members, 'affiliation'));
+                    _.each(affiliations, function (affiliation) {
+                        var iq = $iq({to: room_jid, type: "set"})
                             .c("query", {xmlns: Strophe.NS.MUC_ADMIN});
                         _.each(members, function (member) {
+                            if (member.affiliation !== affiliation) {
+                                return;
+                            }
                             iq.c("item", {
                                 'affiliation': member.affiliation,
                                 'jid': member.jid
@@ -617,7 +623,8 @@
                             }
                             iq.up();
                         });
-                    return converse.connection.sendIQ(iq, onSuccess, onError);
+                        converse.connection.sendIQ(iq, onSuccess, onError);
+                    });
                 },
 
                 marshallAffiliationIQs: function () {