I just realised that when you supply criteria for a getMany:
$xpdoObject->getMany('My_Alias',$New_Criteria);
You actually overwrite the original relational link defined for the alias in the XML. So you must include that original link with the new criteria:
$xpdoObject->getMany('My_Alias',array('originalField'=>'originalValue', 'newCriteriaField'=>'newCriteriaValue' [ etc etc ]);
Haven’t tested this on getOne() yet...
XPDO from svn dated 8 Sep 2009, MODx 1.0, apache 2.2, php 5.