### 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
Atom wt_atom = XInternAtom(x11_display, "_NET_WM_WINDOW_TYPE", False);
			if (wt_atom != None && type_atom != None) {
				XChangeProperty(x11_display, wd.x11_window, wt_atom, XA_ATOM, 32, PropModeReplace, (unsigned char *)&type_atom, 1);
			}
		}
		_update_size_hints(id);
#if defined(VULKAN_ENABLED)
		if (context_vulkan) {
			Error err = context_vulkan->window_create(id, p_vsync_mode, wd.x11_window, x11_display, win_rect.size.width, win_rect.size.height);
			ERR_FAIL_COND_V_MSG(err != OK, INVALID_WINDOW_ID, "Can't create a Vulkan window");
		}
#endif
#ifdef GLES3_ENABLED
		if (gl_manager) {
			Error err = gl_manager->window_create(id, wd.x11_window, x11_display, win_rect.size.width, win_rect.size.height);
			ERR_FAIL_COND_V_MSG(err != OK, INVALID_WINDOW_ID, "Can't create an OpenGL window");
			window_set_vsync_mode(p_vsync_mode, id);
		}
#endif
		
		XFlush(x11_display);
		XSync(x11_display, False);
		
	}
	window_set_mode(p_mode, id);
	
	{
		XWindowAttributes xwa;
		XSync(x11_display, False);
		XGetWindowAttributes(x11_display, wd.x11_window, &xwa);