Did hiding the element this way work when it wasn't being overlaid?! The css class is "blueprint-grid" which makes me wonder if this is a grid element that you're trying to hide.
Yes, the element is being hid this way when it isn't being overlaid. That being said, that element had the incorrect css class assigned to it. I removed the "blueprint-grid" value and assigned the correct css class to it. The element being hid in this example was a layout widget type. Correcting the css class had no affect on the process. The layout element is still hidden on the initial display but is appearing when overlaid with a window.
I couldn't spend any more time to figure this out so I created a work around. Instead of trying to re-hide the underlying fields I just change the opacity of the window mask screen so that the fields underneath do not bleed through. I only change the opacity if there were fields that were hidden otherwise the window mask screen appears as normal.