QWindow with Popup flags can not catch mouse event on Debian9 + Gnome

There is a bug I found when I develop my whiteboard application for linux with qt, and that's really confuse me, and I need Qt engineer's help me to fix it. on Debian9 with Gnome3, if some window (QWindow) layer on the same position, the bug would present: some window with Qt::Popup flags can not catch mouse event there.
And here is a demo I demonstrate the presence of this bug. I try to show 3 windows on the same position, the 1st window with titlebar, and the other would set Qt::Popup flags. There would be high probability that these two window on the top can not catch mouse event(move the 1st window away and you would found it), and this bug I only found on Debian9, the other Linux distribution like Ubuntu, CentOs not happen at all.

As my deadline close, I need to fix this issue as soon as possible.
thanks
shengte wang