### 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
ERR_FAIL_COND(!windows.has(p_window));
	WindowData &wd = windows[p_window];
	if (p_enabled && !window_get_flag(WINDOW_FLAG_BORDERLESS, p_window)) {
		
		Hints hints;
		Atom property;
		hints.flags = 2;
		hints.decorations = 0;
		property = XInternAtom(x11_display, "_MOTIF_WM_HINTS", True);
		if (property != None) {
			XChangeProperty(x11_display, wd.x11_window, property, property, 32, PropModeReplace, (unsigned char *)&hints, 5);
		}
	}
	if (p_enabled) {
		
		_update_size_hints(p_window);
	}
	
	XEvent xev;
	Atom wm_state = XInternAtom(x11_display, "_NET_WM_STATE", False);
	Atom wm_fullscreen = XInternAtom(x11_display, "_NET_WM_STATE_FULLSCREEN", False);
	memset(&xev, 0, sizeof(xev));
	xev.type = ClientMessage;
	xev.xclient.window = wd.x11_window;
	xev.xclient.message_type = wm_state;
	xev.xclient.format = 32;
	xev.xclient.data.l[0] = p_enabled ? _NET_WM_STATE_ADD : _NET_WM_STATE_REMOVE;
	xev.xclient.data.l[1] = wm_fullscreen;
	xev.xclient.data.l[2] = 0;