Hi Marcin,
We did some testing of this and it appears to only show up if the desired height is smaller than the MinHeight you specify. What's happening is that we have to do some API tweaks to the RibbonWindow to get it to allow WPF to support rendering in the non-client area of the window, for the QAT, etc. Unfortunately those API tweaks cause a couple subtle negative side effects with how tall Windows thinks the window is. Unfortunately your issue isn't something we can really fix at this time.
That being said, there is a workaround. If you take off the MinHeight on the RibbonWindow and instead put MinHeight on your root child control of the Window, it will work without displaying the black box.