I already posted my versions in the subtitle, but here it goes again.
Fences 4.0.72, Windows 11 22H2 (OS Build 22621.819)
In fact there are two shortcuts that do not display. The shortcut to MS Flight Simulator is created by going into the Xbox app, right-clicking on the game and choosing "Create desktop shortcut". The shortcut to the JA-100-Link application was created by the program installer, and there is nothing strange with that particular shortcut.
The shortcuts are displayed on the desktop when Fences are disabled. Check the following two screenshots where the two non-displayed files are highlighted:
Fences enabled: https://www.dropbox.com/s/xvvv9ydem26394z/With%20Fences.png?dl=0
Fences disabled: https://www.dropbox.com/s/rqx2nf8pzicd7yv/Without%20Fences.png?dl=0
Screenshot of shortcut properties for JA-100-Link: https://www.dropbox.com/s/ibs5vij3tgkibrm/JA-100%20Link.png?dl=0