I can confirm that, have seen such, too.
Particularly with Midnight Commander not being shown.

My wild guess is that there is some (undocumented?) setting "Show only
graphical applications" or the like in Gnome or its derivatives.
Seems some bug just looking at the mere presence of a Terminal=...
line, and not what it says.

On 4/1/18, Felix Natter <fnat...@gmx.net> wrote:
> Dear xdg members,
>
> a Debian (stretch) user reported an issue where an application (freeplane)
> is not
> shown in the office section. So far I cannot reproduce this (GNOME3),
> but the user reported [1] that it is "fixed" by this change:
>
> --- /usr/share/applications/freeplane.desktop 2016-12-10 12:08:55.000000000
> -0500
> +++ freeplane.desktop 2018-03-20 14:16:27.182938569 -0400
> @@ -2,7 +2,7 @@
>  Version=1.0
>  Name=Freeplane
>  Exec=/usr/bin/freeplane %F
> -Terminal=false
> +#Terminal=false
>  Icon=freeplane
>  Type=Application
>  MimeType=application/x-freeplane;
>
> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=893635
>
> Here is the complete /usr/share/applications/freeplane.desktop:
> [Desktop Entry]
> Version=1.0
> Name=Freeplane
> Exec=/usr/bin/freeplane %F
> Terminal=false
> Icon=freeplane
> Type=Application
> MimeType=application/x-freeplane;
> Categories=Office;
> GenericName=Freeplane
> Comment=A free tool to structure and organise your information with mind
> mapping
> Keywords=Mindmaps; Knowledge management; Organize information;
> Brainstorming; ...;
>
> Do you have any idea what might cause this?
>
> Many Thanks and Best Regards,
> --
> Felix Natter
>
> _______________________________________________
> xdg mailing list
> xdg@lists.freedesktop.org
> https://lists.freedesktop.org/mailman/listinfo/xdg
>
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