I have a number of nodes in the datamanger.
Their order is important for the rendering! e.g. when a segmentation node is UNDER (not a child node, simply lower in the datamanager list) the base image, the segmentation is not visbile!
When you save the MITK Project and load it again, the position of the nodes in the datamanger changes!
You can take this as an example project:
t:\temp\P0031-T4.mitk
Change the positions, save the MITK project again, load it and you will see the position of the nodes changes.
It should not.