We have run across z-indexing issues when mixing 2.2.5 components with 3.0.x windows (and vice-versa), and it has caused us a bit of grief.
The issue arises in the two different WindowManager classes;
Each WindowManager statically accesses the following XDOM classes, respectively;
Now, if you are using a mixture of 2.2.5 and 3.0.x Window derived classes, I believe you can get into a state where the zindex in each of the XDOM classes gets out of sync. End affect is that some components will have a lower z index than their parent container (when the version of component differs from the version of the window), and they can end up "behind" the parent window.
We have been meaning to write this up as a bug, but were trying to head Sven off at the pass with the "supply entry point example where the problem exists". We just haven't had the time to put the example together.