### 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
if (p_position != nullptr) {
		window_position = *p_position;
	} else {
		if (p_screen == SCREEN_OF_MAIN_WINDOW) {
			p_screen = SCREEN_PRIMARY;
		}
		window_position = screen_get_position(p_screen) + (screen_get_size(p_screen) - p_resolution) / 2;
	}
	WindowID main_window = _create_window(p_mode, p_vsync_mode, p_flags, Rect2i(window_position, p_resolution));
	if (main_window == INVALID_WINDOW_ID) {
		r_error = ERR_CANT_CREATE;
		return;
	}
	for (int i = 0; i < WINDOW_FLAG_MAX; i++) {
		if (p_flags & (1 << i)) {
			window_set_flag(WindowFlags(i), true, main_window);
		}
	}
	show_window(main_window);
#if defined(VULKAN_ENABLED)
	if (rendering_driver == "vulkan") {
		
		rendering_device_vulkan = memnew(RenderingDeviceVulkan);
		rendering_device_vulkan->initialize(context_vulkan);
		RendererCompositorRD::make_current();
	}
#endif
	{
		
		XIEventMask all_master_event_mask;