Yes, clean install for part of softwares will cause this bug.

See Also, https://bugs.launchpad.net/ubuntu/+source/gnome-
panel/+bug/1530555

And the reason is simple, the menu from gnome-panel will display a new
item if a new "desktop" file is created in /usr/share/application/
folder, but the menu will check whether "TryExec=" points to a non-exist
file or an invalid link, if so, the menu still hide this item even after
the target that "TryExec=" points to become valid.

One of the following solutions can fix this bug,

1. force dpkg to postpone installing "[DEB]/usr/share/applications/*"
files in the deb package, in order to make the file that "TryExec="
points to become valid first.

2. add a trigger after every dpkg installation finish to force updating
the whole menus.

3. force gnome-panel to ignore "TryExec=" field to let menu item always
show.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-panel in Ubuntu.
https://bugs.launchpad.net/bugs/1518775

Title:
  gnome-panel cannot show newly installed software icons

Status in gnome-panel package in Ubuntu:
  Confirmed

Bug description:
  1) First => sudo apt-get install gnome-session-flashback

  
  2) Then => re-login user with "Gnome Flashback (Metacity)" session

  
  3) Next => install a software that does not exist in gnome-panel menu list 
previously, such as "sudo apt-get install mousepad"

  However, after installion of mousepad, its icons doesn't show in
  gnome-panel menu list. I have to:

  4) killall gnome-panel

  5) gnome-panel &

  Then, the mousepad icon can be shown in gnome-panel menu list.

  This might be caused by forgetting to update icon menu list from
  gnome-panel

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: gnome-panel 1:3.18.1-1ubuntu3
  ProcVersionSignature: Ubuntu 4.2.0-19.23-generic 4.2.6
  Uname: Linux 4.2.0-19-generic x86_64
  ApportVersion: 2.19.2-0ubuntu6
  Architecture: amd64
  CurrentDesktop: GNOME-Flashback:Unity
  Date: Mon Nov 23 06:13:43 2015
  GsettingsChanges:
   
  JournalErrors:
   Error: command ['journalctl', '-b', '--priority', 'warning'] failed with 
exit code 1: Hint: You are currently not seeing messages from other users and 
the system.
         Users in the 'systemd-journal' group can see all messages. Pass -q to
         turn off this notice.
   No journal files were opened due to insufficient permissions.
  SourcePackage: gnome-panel
  UpgradeStatus: No upgrade log present (probably fresh install)

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