Attached is a self-contained 80 line test. In the test, Foo has an one to one relation to Bar. There is a null value in the foreign key column (at least one Foo without a Bar). And the relation is being used via this DQL:
Doctrine_Query::create()->from('Foo f')->leftJoin('f.Bar b')->execute();
At around line 254 of Doctrine_Hydrator_Graph/Graph.php, the hydrator sets the value of the relation column to Doctrine_Null if there is no related record:
$prev[$parent][$relationAlias] = $this->getNullPointer();
This causes Doctrine_Record to check if the value of the foreign key field was updated, which it does by calling Doctrine_Record::_isValueModified(). However, that method considers an update from null to Doctrine_Null as a modification. So, the record (and eventually the entire Collection returned) is marked as Doctrine_Record::STATE_DIRTY, even though it contains no modifications. This occurs during hydration, so the caller never sees the record as being clean.
The workaround I'm using is to subclass Doctrine_Record, and return false from _isValueModified() when moving from null to Doctrine_Null. But I think this could also be fixed in the hydrator.