Not everyone has deleted the registry keys which disable the viewing of certain extensions (including .lnk), and if those registry keys are in affect, the command prompt will not see those extensions, nor will the Windows GUI. The registry keys were NeverShowExt if I am not mistaken, but before any registry modification should be made (one should really avoid doing them anyway unless you know EXACTLY what you are doing and how it will affect your computer), always, ALWAYS, preform a backup of your registry.