### 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
XEvent config_event;
	while (XCheckTypedEvent(x11_display, ConfigureNotify, &config_event)) {
		_window_changed(&config_event);
	}
	events_thread.start(_poll_events_thread, this);
	_update_real_mouse_position(windows[MAIN_WINDOW_ID]);
#ifdef DBUS_ENABLED
	screensaver = memnew(FreeDesktopScreenSaver);
	screen_set_keep_on(GLOBAL_GET("display/window/energy_saving/keep_screen_on"));
	portal_desktop = memnew(FreeDesktopPortalDesktop);
#endif
	r_error = OK;
}
DisplayServerX11::~DisplayServerX11() {
	
	Window x11_main_window = windows[MAIN_WINDOW_ID].x11_window;
	_clipboard_transfer_ownership(XA_PRIMARY, x11_main_window);
	_clipboard_transfer_ownership(XInternAtom(x11_display, "CLIPBOARD", 0), x11_main_window);
	events_thread_done.set();
	events_thread.wait_to_finish();
	
	for (KeyValue<WindowID, WindowData> &E : windows) {
#ifdef VULKAN_ENABLED
		if (context_vulkan) {
			context_vulkan->window_destroy(E.key);
		}
#endif
#ifdef GLES3_ENABLED
		if (gl_manager) {