### 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_
	ERR_FAIL_COND_V(!windows.has(p_window), WINDOW_MODE_WINDOWED);
	const WindowData &wd = windows[p_window];
	if (wd.fullscreen) { 
		if (wd.exclusive_fullscreen) {
			return WINDOW_MODE_EXCLUSIVE_FULLSCREEN;
		} else {
			return WINDOW_MODE_FULLSCREEN;
		}
	}
	
	
	if (_window_maximize_check(p_window, "_NET_WM_STATE")) {
		return WINDOW_MODE_MAXIMIZED;
	}
	{
		if (_window_minimize_check(p_window)) {
			return WINDOW_MODE_MINIMIZED;
		}
	}
	
	return WINDOW_MODE_WINDOWED;
}
void DisplayServerX11::window_set_flag(WindowFlags p_flag, bool p_enabled, WindowID p_window) {