Fixed in r24723
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24723

Reverted in r24734
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24734

The issue is still there Slicer 4.7.0-2017-09-26 on Windows10.

The test scene is available here:
https://1drv.ms/u/s!Arm_AFxB9yqHsKtWHFuufICWI0mAww

Another way to reproduce this:

[quote="mholden8, post:11, topic:2153"]
experience the same issue as Nathan. Here are the steps that I can do to reproduce the issue (latest Slicer nightly 2018-03-05, Windows 10):

Open fresh Slicer.
Create a transform node. Call it FirstTransformNode.
Save the scene.
Create a another transform node. Call it SecondTransformNode.
Make SecondTransformNode the parent of FirstTransformNode.
Save the scene.
Clear the scene.
Reload the saved scene created in Step 6.

In the reloaded scene, SecondTransformNode does not appear to be the parent of FirstTransformNode in the Data module GUI (transform hierarchy tab). Likewise, in the Transforms module, FirstTransformNode does not appear to be transformed by SecondTransformNode in the GUI. But I observe that if I check the parent node of FirstTransformNode through the Python interactor, it is SecondTransformNode. See commands below:

firstTransformNode = slicer.util.getNode( “FirstTransformNode” )

parentTransformNode = firstTransformNode.GetParentTransformNode()

print( parentTransformNode )
[/quote]

See more discussion here:
https://discourse.slicer.org/t/transform-hierarchy-in-data-module-not-showing-multiple-transforms-correctly/2153/11

Even simpler way to reproduce:

1. Start Slicer or close scene

2. Copy-paste to Python console:
   <pre>
   sceneXMLString = """
   <MRML version="Slicer4.4.0" userTags="">
   <LinearTransform
   id="vtkMRMLLinearTransformNode4" name="FirstTransformNode" hideFromEditors="false" selectable="true" selected="false" transformNodeRef="vtkMRMLLinearTransformNode5" references="transform:vtkMRMLLinearTransformNode5;" userTags="" matrixTransformToParent="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" ></LinearTransform>
   <LinearTransform
   id="vtkMRMLLinearTransformNode5" name="SecondTransformNode" hideFromEditors="false" selectable="true" selected="false" references="" userTags="" matrixTransformToParent="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" ></LinearTransform>
   </MRML>
   """
   slicer.mrmlScene.SetLoadFromXMLString(1);
   slicer.mrmlScene.SetSceneXMLString(sceneXMLString)
   slicer.mrmlScene.Import()
   </pre>

If parent transform node is listed in the scene first then the hierarchy appears correctly:
<pre>
sceneXMLString = """
<MRML version="Slicer4.4.0" userTags="">
<LinearTransform
id="vtkMRMLLinearTransformNode5" name="SecondTransformNode" hideFromEditors="false" selectable="true" selected="false" references="" userTags="" matrixTransformToParent="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" ></LinearTransform>
<LinearTransform
id="vtkMRMLLinearTransformNode4" name="FirstTransformNode" hideFromEditors="false" selectable="true" selected="false" transformNodeRef="vtkMRMLLinearTransformNode5" references="transform:vtkMRMLLinearTransformNode5;" userTags="" matrixTransformToParent="1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1" ></LinearTransform>
</MRML>
"""
slicer.mrmlScene.SetLoadFromXMLString(1);
slicer.mrmlScene.SetSceneXMLString(sceneXMLString)
slicer.mrmlScene.Import()
</pre>

Submitted a pull request with a potential fix:

https://github.com/Slicer/Slicer/pull/915

Fix committed r27077

Thanks Andras

Would it be possible to evaluate the work that was already done as part of issue 0004081

More specifically, this topic is getting us closer I think:

https://github.com/jcfr/Slicer/compare/add-vtkEventSpy...jcfr:4081-ensure-reference-are-up-to-date-on-import

I completely agree that it should be done, but I have priority tasks now. 0004081 is still open, so it should keep this task on our radar.