### 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
Rect2i srect = screen_get_usable_rect(p_screen);
		Point2i wpos = window_get_position(p_window) - screen_get_position(window_get_current_screen(p_window));
		Size2i wsize = window_get_size(p_window);
		wpos += srect.position;
		if (srect != Rect2i()) {
			wpos.x = CLAMP(wpos.x, srect.position.x, srect.position.x + srect.size.width - wsize.width / 3);
			wpos.y = CLAMP(wpos.y, srect.position.y, srect.position.y + srect.size.height - wsize.height / 3);
		}
		window_set_position(wpos, p_window);
	}
}
void DisplayServerX11::window_set_transient(WindowID p_window, WindowID p_parent) {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(p_window == p_parent);
	ERR_FAIL_COND(!windows.has(p_window));
	WindowData &wd_window = windows[p_window];
	WindowID prev_parent = wd_window.transient_parent;
	ERR_FAIL_COND(prev_parent == p_parent);
	DEBUG_LOG_X11("window_set_transient: %lu (%u), prev_parent=%u, parent=%u\n", wd_window.x11_window, p_window, prev_parent, p_parent);
	ERR_FAIL_COND_MSG(wd_window.on_top, "Windows with the 'on top' can't become transient.");
	if (p_parent == INVALID_WINDOW_ID) {
		
		ERR_FAIL_COND(prev_parent == INVALID_WINDOW_ID);
		ERR_FAIL_COND(!windows.has(prev_parent));
		WindowData &wd_parent = windows[prev_parent];
		wd_window.transient_parent = INVALID_WINDOW_ID;
		wd_parent.transient_children.erase(p_window);
		XSetTransientForHint(x11_display, wd_window.x11_window, None);
		XWindowAttributes xwa;
		XSync(x11_display, False);