In system/core/dynamic/BeanPopulator.cfc you loop over memento keys. These are obtained by the getRelationshipMetaData method, but these method doesn't loop over parent objects.
I made a fix which I already sent to Louis (15-5-2014) but probably it got lost somewhere. For v4 I created a new fix which also works for Lucee.
I think the same beanpopulator is also used in Cachebox, Logbox and wirebox, but I think this bug is only showing in core for objects created by coldbox users.