Comment 4 for bug 1253922

I was able to reproduce the problem after I installed a linux VM.

Some further digging via google tells me that Qt is broken on several *nix systems, not respecting that modeless dialogs are supposed to remain on top of their parent window. Fortunately there is a "fix" that purportedly works most of the time (and works for me on my Debian VM), where the program (calibre) explicitly informs the window manager that the modeless dialog is to remain on top.