I have seen and experienced problems with app.config/web.config where I had changed the order of elements and the app stopped working. I believe I fixed the problem by looking at machine.config and following the order in there.
One example is the following question: Common.Logging config exception
The issue was resolved by changing the order the elements appear in the file.
So, the question is, does the order of elements matter?
It appears to me it does. If it does, is it documented anywhere, an xsd schema maybe?