we just found a bug in mitkSceneReaderV1::LoadScene(...).
Create a scene with two (2) or more data nodes with the same parent and the following properties:
"fixed layer" = true
"layer" = 100 (above 10, so not set in Property plugin)
Then store as .mitk project.
When reading in the project mitkSceneReaderV1 will add the apropriate number of entries into local variable "DataNodes" but when building up member variable m_OrderedNodePairs the amount of entries will differ. The reason is that the information about the sourceUID of each node is inserted into this list by the key "layer" and as this layer is not distinct, there will be a double entry for the layer number (->example 100). ->m_OrderedNodePairs contains at  100 on pair first (layer) and on second a list of with entries containing the same OBJECT_<timestamp> value.
The effect is that in the console the warning: "Encountered node that is not part of a directed graph structure. Will be added to DataStorage without parents" with following errors stating that the reading process caused errors...
In the DataManager the second data node of the pair of equal properties (fixed layer and layer value) is not present and the children of this node are hung into toplevel hierachy the the DataManager.
Perhaps this bug is gone with the new IO mechanism?
I haven't found a similar bug description so far, so I thing this but yet was not found.
The reason for us to use fixed layering is to control the rendering order of several meshes that lie very close to one another an thus proper visualization is dependent on the order of rendering.
Keep up the great work! ;)
P.S. I will provide a project file to reproduce...