The source of my problem is the Open Inventor implementation from SoQt/Coin3D. When you have two different hierarchies, a SoNode::getByName(...) seems not work properly. It is not ensured from which SoNode is returned. It can be from any hierarchy even if these hierarchies are in different classes and namespaces.
Well this is quite abstract for me, since I don't know your code.
Over a forum it is hard to look for problems in cases like these based on symptoms, because the complexity, and the inability to see the full code.
You should try and debug your problem and reduce it to an specific problem domain, not a symptom.
Probably then we will be more able to help.
Good luck!