PyQt6: Popup QMainWindow sometimes "missing" clicks even if opened and activated

I’m building a macOS menu bar extra (a.k.a. system tray) app using PyQt6. When clicking the menu bar icon, a popup window appears, which is a QMainWindow with the Qt.WindowType.Popup window flag set.

I’m noticing sporadic issues where the popup window is unresponsive even though it is open. Sometimes, clicking on a QPushButton inside the popup, or an action on the QMenu, causes it to close abruptly without the clicked signal being invoked on the button or the triggered action on a menu item (i.e., clicks are sometimes being “missed”). The popup window contains a QTreeWidget which I’ve styled with QSS so that hovering over a QTreeWidgetItem will cause it to be highlighted; sometimes the highlight doesn’t appear, suggesting that the open popup window is ignoring user interaction.

I have been able to reproduce these issues on macOS 15 Sequoia and macOS 26 Tahoe, using a mouse (on a Mac Mini) and a trackpad (on a MacBook Air). In the latter case, the missed clicks tend to be more frequent if the “tap to click” setting is enabled on the trackpad.

I tried explicitly calling the activateWindow() method on the QMainWindow object for the popup window; as well as calling grabMouse() (and releaseMouse() in the overridden method closeEvent()). I also ensured that the widgets within the popup window have its self object passed to their constructors. Despite these attempted fixes, the issue is still occurring.

What should I be doing to ensure that the popup window is consistently capturing mouse input when it’s opened? What gotchas and caveats that I missed that could be causing this issue?