Wierd mouse-over behaviour using GUI.Matrix with GUI.Window

Hello, When the current screen resolution is lower than a predefined value, we scale down the whole UI using GUI.Matrix. Everything shows up fine, but when GUI.Window is used, gui elements with Hover style detect mouse incorrectly. Also Rect.Contains starts failing.

This started happening after upgrading from Unity 4.1.0 to 4.2.0. I noticed there is a new GUI.ModalWindow from 4.1.2, which when used, does not produce the above problems as GUI.Window.

However using GUI.ModalWindow is not always preferrable.

Anyone bumbed into this?