I opened a Budget Report from the Reports menu. Maximized the window. Clicked the Options button on the menu bar. At first, I thought the Report Options dialog was randomly falling into the background and out of view immediately after opening. With some extra testing I realized that every time I hover any button on the menu bar, the GnuCash window is brought to the foreground and hides all dialog windows. This can also happen if the mouse innocently lingers over the Options button after clicking it. Very unintuitive and mildly painful.
This seems to be only on Windows as I can not reproduce on my Linux VM. What I have observed is that when you hover the mouse on the menu bar and the tooltip is displayed any windows/dialogues that do not have the 'transient parent setting' are affected and sent into the background. This can be observed by it not affecting the 'Saved Report Configuration' when it is open which does have the setting. Not really sure if any thing can be done about this or if it is a Gtk problem.
Confirmed bug in v3.4.
Seems to be fixed in v3.5.