Editor Shortcuts reset after restarting Godot

[prominentdetail]

Godot version

4.0

System information

windows 10

Issue description

If you change only the modifier keys such as alt,shift,ctrl of a shortcut, it won't save these changes when godot is restarted. They will be reset to the previous settings.
It only saves if you change the actual key(not the modifiers).

Steps to reproduce

Got to the Editor settings and change the modifier keys for a shortcut.. then restart godot and check it again. They will be reset to previous settings.

Minimal reproduction project

any

[akien-mga]

CC @EricEzaM @bruvzg