Ah, I finally found what you're talking about. This thing has multiple elements called Properties. There is a Properties tab above the left pane. When a measure is selected, a Measure item appears there: a trash button to delete selected measures and a button to insert measures.
You're talking about a right click context menu which has a Measure Properties command. That indeed opens behind the main window. (Is this using GTK+? I regularly see this issue in GTK+ programs on Windows like GIMP; it's been there for at least 15 years.)
I see that I can set the actual time of a measure to, say 1/4 which creates a one beat pickup measure if it's the first measure.
No it's all Qt. I've tried fixing a few cases but yeah, seems something fundamental to the Qt library.
I'd like to think that dialog will probably go away and be rolled into the properties pane, which I gather is Martin's (tantacrul's) preference.
When a program that has never serviced its Windows message pump runs another program via CreateProcess, and that program creates a window, that program's window fails to come to the foreground.
This goes away with a dummy call to TranslateMessage.
I just assumed it was because the window owner wasn't set properly (but it's a long time since I did windows desktop app development).
Strangely I can't reproduce the problem now - you can certainly send the dialog behind the parent, but it comes up above it initially as expected.
What is a problem for me though is that the measure properties dialog opens up behind the main window...