### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
WindowID window_id = MAIN_WINDOW_ID;
	
	for (const KeyValue<WindowID, WindowData> &E : windows) {
		if (event->xany.window == E.value.x11_window) {
			window_id = E.key;
			break;
		}
	}
	Rect2i new_rect;
	WindowData &wd = windows[window_id];
	if (wd.x11_window != event->xany.window) { 
		return;
	}
	
	wd.fullscreen = _window_fullscreen_check(window_id);
	wd.minimized = _window_minimize_check(window_id);
	wd.maximized = _window_maximize_check(window_id, "_NET_WM_STATE");
	{
		
		int x = 0, y = 0;
		Window child;
		XTranslateCoordinates(x11_display, wd.x11_window, DefaultRootWindow(x11_display), 0, 0, &x, &y, &child);
		new_rect.position.x = x;
		new_rect.position.y = y;
		new_rect.size.width = event->xconfigure.width;
		new_rect.size.height = event->xconfigure.height;