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This issue is still happening in 4.2 - there is nothing fancy in our window, a couple of grids and a form. We are not rendering into the window. Unfortunately there's too much in the window/form to produce a test case. After fighting it for a while and seeing the closed ticket, I fixed it by setting the zindex in a style for the window so it wouldn't be auto. Not an elegant fix but we've already lost enough time fighting it - better than no work around.