Make sure that you have the auto-increment flag set when setting up the object in the method setTableDefinition()(or in the corresponding YAML configuration file). If this flag is not set, Doctrine will not know to update it. You should have something similar to this:
$this->hasColumn('id', 'integer', 4, array(
'type' => 'integer',
'length' => 4,
'fixed' => false,
'unsigned' => true,
'primary' => true,
'autoincrement' => true
)
);