Can not close Floating Panels like Project Settings

### Tested versions

Reprodutable in 4.6
had it in the Beta Release, and i have it in the official 4.6

Was not pressent in any olther version (4.X)

### System information

Godot v4.6.stable unknown - EndeavourOS #1 SMP PREEMPT_DYNAMIC Sun, 11 Jan 2026 17:10:53 +0000 on Wayland - X11 display driver, Multi-window, 1 monitor - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1650 (nvidia; 580.126.09) - 11th Gen Intel(R) Core(TM) i5-11400H @ 2.70GHz (12 threads) - 15.39 GiB memory

### Issue description

Can not close windows like the Shortcut Panel , project settings, Shortcut. Any floating panel actually.
even tho i press the X (close button), nothing happens

and i'm forced to kill the entire Godot Procces from Task Manager

### Steps to reproduce

Does not always happen. Most recently got it trying to rebind the shortcut for FileSystem

from Alt + F, cuz i use it for something else, to Ctrl + Space

After the "Listening BOX" try to press OK and nothing Happens, and i cannot close the window

### Minimal reproduction project (MRP)

it happens in any 4.6 project.

Start by reproducing the issue in a Godot 4.6 project while opening Project Settings or the shortcut panel and attempting to close or confirm the floating window. The fix is complete when these panels reliably respond to their close and confirmation actions without requiring the Godot process to be terminated.

Written by the indexing model from the issue text.