### 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
_THREAD_SAFE_METHOD_
	WindowData &wd = windows[MAIN_WINDOW_ID];
	int (*oldHandler)(Display *, XErrorEvent *) = XSetErrorHandler(&set_icon_errorhandler);
	Atom net_wm_icon = XInternAtom(x11_display, "_NET_WM_ICON", False);
	if (p_icon.is_valid()) {
		Ref<Image> img = p_icon->duplicate();
		img->convert(Image::FORMAT_RGBA8);
		while (true) {
			int w = img->get_width();
			int h = img->get_height();
			if (g_set_icon_error) {
				g_set_icon_error = false;
				WARN_PRINT("Icon too large, attempting to resize icon.");
				int new_width, new_height;
				if (w > h) {
					new_width = w / 2;
					new_height = h * new_width / w;
				} else {
					new_height = h / 2;
					new_width = w * new_height / h;
				}
				w = new_width;
				h = new_height;
				if (!w || !h) {
					WARN_PRINT("Unable to set icon.");
					break;
				}
				img->resize(w, h, Image::INTERPOLATE_CUBIC);