### 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 (config_name.length() == 0) {
				class_str = "Godot_Engine";
			} else {
				class_str = config_name.utf8();
			}
		} else {
			class_str = "Godot";
		}
		classHint->res_class = class_str.ptrw();
		classHint->res_name = name_str.ptrw();
		XSetClassHint(x11_display, wd.x11_window, classHint);
		XFree(classHint);
	}
}
void DisplayServerX11::set_context(Context p_context) {
	_THREAD_SAFE_METHOD_
	context = p_context;
	for (KeyValue<WindowID, WindowData> &E : windows) {
		_update_context(E.value);
	}
}
void DisplayServerX11::set_native_icon(const String &p_filename) {
	WARN_PRINT("Native icon not supported by this display server.");
}
bool g_set_icon_error = false;
int set_icon_errorhandler(Display *dpy, XErrorEvent *ev) {
	g_set_icon_error = true;
	return 0;
}
void DisplayServerX11::set_icon(const Ref<Image> &p_icon) {