The problem here is part of the resource save function magento checks if the primary key is set to auto increment and then removes it from the data being saved if this is the case.
In Mage_Core_Model_Resource_Db_Abstract::save
you can see how it deals with $this->_isPkAutoIncrement
/**
* Not auto increment primary key support
*/
if ($this->_isPkAutoIncrement) {
$data = $this->_prepareDataForSave($object);
unset($data[$this->getIdFieldName()]);
$this->_getWriteAdapter()->update($this->getMainTable(), $data, $condition);
} else {
$select = $this->_getWriteAdapter()->select()
->from($this->getMainTable(), array($this->getIdFieldName()))
->where($condition);
if ($this->_getWriteAdapter()->fetchOne($select) !== false) {
$data = $this->_prepareDataForSave($object);
unset($data[$this->getIdFieldName()]);
if (!empty($data)) {
$this->_getWriteAdapter()->update($this->getMainTable(), $data, $condition);
}
} else {
$this->_getWriteAdapter()->insert($this->getMainTable(), $this->_prepareDataForSave($object));
}
}
So to fix my issue I simply have to set $_isPkAutoIncrement
on my Model's resource to false and Magento will keep the PK in the data and save it into the table.