faster GUI in unity 4.0.0 behaves differently than in 3.x?

Hi. I posted the following question on Unity3D Questions but I later found this forum which seems much more active, so here goes:

Is it possible that the faster GUI shipped with Unity 4.x behaves differently in some cases? I had a script that relied on the MakeWindow function to be called even in “-batchmode” mode, and when I upgraded to 4.0.0 the function is never called.

Where can I find all the changes to GUI so I can fix my code accordingly? Thanks, Manuel

This is the only info I found; no detailed changelog available:

(taken from http://unity3d.com/unity/whats-new/unity-4.0)

As for the speed, I noticed the significant gain and also the GC working better. Here is the thread related to this topic.