I have this piece of code in my decorator, which is mostly copy-paste from FormScaffolder to add a field for the many_many attribute Contacts.

public function updateCMSFields(FieldSet &$fields) {
	$component = 'Contact';
	$relationship = 'Contacts';
	$relationshipFields = $this->getRelationshipFields();
	$filterWhere = $this->owner->getManyManyFilter($relationship, $component);
	$filterJoin = $this->owner->getManyManyJoin($relationship, $component);

	$dom =  new DataObjectManager($this->owner,
			$relationship,
			$component,
			$relationshipFields,
			"getCMSFields_forPopup",
			$filterWhere,
			'',
			$filterJoin
	);
	$tab = $fields->findOrMakeTab('Root.Main.Contacts',
			singleton($component)->i18n_plural_name());
	$tab->push($dom);
}

Existing contacts show up in the field as expected. But if I add a new contact, the contact it is saved in the Contact table, as expected, but the relation is not saved in the relationship table. If I replace DataObjectManager with ComplexTableField it works as it should.