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I couldn't reproduce with the Hero/SecretIdentity example DomainObjects, so I've simplified the models which trigger the issue in our project and included them here (PHP 5.4 only, so this testcase might fail on 5.3).
Differences between Hero/SecretIdentity and Veldwerkdag/Project are the definition of the primary key (Sequence vs. Integer) and in the belongsTo relationship we define both local and foreign keys.
Please
var_dump($schema->hash($object, array($this->local)))
inRelationships/BelongsTo.php
to see the issue. (Not sure how I could let the test fail on this)