For 0000001, it looks like a new volume display node is being created on scene restore, rather than using the one already defined for the label map. The back trace shows a problem with an event being caught by the slice layer logic, leading to this snippet of code:
Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx at line 343:
// TODO: this is a hack
vtkErrorMacro("UpdateNodeReferences: Volume Node " << this->VolumeNode->GetID() << " doesn't have a display node, adding one.");

In the back trace at frame 19, the node id is vtkMRMLScalarVolumeNode4 which is the label map volume.

vtkMRMLDisplayableNode::UpdateScene clears out all the display nodes first.

Back trace from creating the new label map display node:
(gdb) bt
#0 vtkMRMLLabelMapVolumeDisplayNode::vtkMRMLLabelMapVolumeDisplayNode (this=0x715e5f0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLLabelMapVolumeDisplayNode.cxx:33
0000001 0x00007f5fe94cb8c5 in vtkMRMLLabelMapVolumeDisplayNode::New () at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLLabelMapVolumeDisplayNode.cxx:28
0000002 0x00007f5fefafe7e4 in vtkMRMLSliceLayerLogic::UpdateNodeReferences (this=0x2e9fe80) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx:367
0000003 0x00007f5fefafee13 in vtkMRMLSliceLayerLogic::UpdateTransforms (this=0x2e9fe80) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx:451
0000004 0x00007f5fefafe0a1 in vtkMRMLSliceLayerLogic::UpdateLogic (this=0x2e9fe80) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx:236
0000005 0x00007f5fefafe224 in vtkMRMLSliceLayerLogic::OnMRMLNodeModified (this=0x2e9fe80, node=0x353b980)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx:277
0000006 0x00007f5fefad26e7 in vtkMRMLAbstractLogic::ProcessMRMLNodesEvents (this=0x2e9fe80, caller=0x353b980, event=33)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLAbstractLogic.cxx:448
0000007 0x00007f5fefafe153 in vtkMRMLSliceLayerLogic::ProcessMRMLNodesEvents (this=0x2e9fe80, caller=0x353b980, event=33, callData=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx:256
0000008 0x00007f5fefad1b1b in vtkMRMLAbstractLogic::MRMLNodesCallback (caller=0x353b980, eid=33, clientData=0x2e9fe80, callData=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Logic/vtkMRMLAbstractLogic.cxx:184
---Type <return> to continue, or q <return> to quit---
0000009 0x00007f5fde0f45f7 in vtkCallbackCommand::Execute (this=0x2ea00c0, caller=0x353b980, event=33, callData=0x0)
at /projects/birn/nicole/Slicer4/S4-SuperBuild/VTK/Common/vtkCallbackCommand.cxx:42
0000010 0x00007f5fe941c31c in vtkEventBroker::InvokeObservation (this=0xdd91e0, observation=0x72a1c30, callData=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkEventBroker.cxx:853
0000011 0x00007f5fe941b9c1 in vtkEventBroker::ProcessEvent (this=0xdd91e0, observation=0x72a1c30, caller=0x353b980, eid=33, callData=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkEventBroker.cxx:707
0000012 0x00007f5fe941c8fb in vtkEventBroker::Callback (caller=0x353b980, eid=33, clientData=0x72a1c30, callData=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkEventBroker.cxx:928
0000013 0x00007f5fde0f45f7 in vtkCallbackCommand::Execute (this=0x72a1f90, caller=0x353b980, event=33, callData=0x0)
at /projects/birn/nicole/Slicer4/S4-SuperBuild/VTK/Common/vtkCallbackCommand.cxx:42
0000014 0x00007f5fde1d4c5d in vtkSubjectHelper::InvokeEvent (this=0x5f4d3f0, event=33, callData=0x0, self=0x353b980)
at /projects/birn/nicole/Slicer4/S4-SuperBuild/VTK/Common/vtkObject.cxx:602
0000015 0x00007f5fde1d516d in vtkObject::InvokeEvent (this=0x353b980, event=33, callData=0x0) at /projects/birn/nicole/Slicer4/S4-SuperBuild/VTK/Common/vtkObject.cxx:770
0000016 0x00007f5fde1d533c in vtkObject::Modified (this=0x353b980) at /projects/birn/nicole/Slicer4/S4-SuperBuild/VTK/Common/vtkObject.cxx:836
---Type <return> to continue, or q <return> to quit---
0000017 0x00007f5fe9c02bc7 in vtkMRMLNode::Modified (this=0x353b980) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLNode.h:342
0000018 0x00007f5fe94837b1 in vtkMRMLDisplayableNode::SetAndObserveNthDisplayNodeID (this=0x353b980, n=0, displayNodeID=0x0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLDisplayableNode.cxx:326
0000019 0x00007f5fe9482c1e in vtkMRMLDisplayableNode::UpdateScene (this=0x353b980, scene=0xe867b0)
at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLDisplayableNode.cxx:171
0000020 0x00007f5fe96329b0 in vtkMRMLVolumeNode::UpdateScene (this=0x353b980, scene=0xe867b0) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLVolumeNode.cxx:673
0000021 0x00007f5fe95aaaa3 in vtkMRMLSceneViewNode::RestoreScene (this=0x2d62890) at /projects/birn/nicole/Slicer4/Slicer4/Libs/MRML/Core/vtkMRMLSceneViewNode.cxx:490

Possible fix might be to check IsRestoring() on the scene before creating new nodes in vtkMRMLSliceLayerLogic::UpdateNodeReferences, possibly checking for it in vtkMRMLSliceLayerLogic::OnMRMLNodeModified.
Update: didn't work.

Why vtkMRMLSliceLayerLogic thinks there is no display node associated with the displayable node (ScalarVolumeNode4) ?

2) Volume Rendering failed when "Right Kidney..." scene view is restored because the scene is loaded using "Add Data" and not "Load Scene". When loading a scene using "Add Data", it creates a duplicate "vtkMRMLViewNode2" and "vtkMRMLCameraNode 2". When restoring, the scene view volume rendering display node is visible only in vtkMRMLViewNode2 which is not the one visible in layout, but vtkMRMLViewNode1.

2a) "Add data" of a scene should be the same as "Load scene" or "Import scene".
optional 2b) "Add data" of a scene adds vtkMRMLViewNode2 however it is vtkMRMLViewNode1 that is visible in layout.

re note 4003 from Julien: because the label map volume node in vtkMRMLDisplayableNode::UpdateScene (backtrace frame 19) calls set and observe display node to NULL while trying to update the node pointers from the node id list.

How is a poor end user to know? This has to be streamlined and clarified, with the end user in mind.

Need to check if changes since April fix the LUT issue.

Any progress here?

Fixed in r21027 and r21033:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21027
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=21033

As of r21056, creating a new scene is no longer needed, VR backward compatibility has been added for scenes older than r20474.