Ahmed,
Just guessing at the problem but are you launching eclipse from the command 
line? If you are launching as root from the command line the eclipse.desktop 
file doesn't take effect. This file is only for launching from the dash. 

To launch from the command line with this fix type in:
env UBUNTU_MENUPROXY= /opt/eclipse/eclipse

(remembering the space after the "=").

Hope that helps

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https://bugs.launchpad.net/bugs/1208019

Title:
  Eclipse menus doesn't show up in Saucy

Status in “eclipse” package in Ubuntu:
  Triaged
Status in “unity-gtk-module” package in Ubuntu:
  Triaged

Bug description:
  ****************
  HOW TO REPRODUCE
  ****************

  1. Run Eclipse.
  2. Move the cursor to the top of the screen.
  3. Click on any of the menu items (File, Edit, Navigate, ...)

  ******************
  EXPECTED BEHAVIOUR
  ******************

  - The content of the submenus show up.

  **************
  REAL BEHAVIOUR
  **************

  - Only the top-level headers are available.
  - Nothing happens when clicking on them
  - They don't show up in the HUD either.

  ***********
  WORK-AROUND
  ***********

  To modify "/usr/share/applications/eclipse.desktop" to look like this:

  [Desktop Entry]
  Type=Application
  Name=Eclipse
  Comment=Eclipse Integrated Development Environment
  Icon=eclipse
  Exec=env UBUNTU_MENUPROXY= eclipse
  Terminal=false
  Categories=Development;IDE;Java;

  ****************
  RELEVANT DETAILS
  ****************

  - Doesn't affect Ubuntu releases prior to 13.10.

  **************
  TECHNICAL INFO
  **************

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: eclipse 3.8.1-1ubuntu1
  ProcVersionSignature: Ubuntu 3.10.0-6.17-generic 3.10.3
  Uname: Linux 3.10.0-6-generic i686
  ApportVersion: 2.11-0ubuntu1
  Architecture: i386
  Date: Sat Aug  3 17:03:55 2013
  InstallationDate: Installed on 2013-07-08 (25 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Alpha i386 (20130708)
  MarkForUpload: True
  PackageArchitecture: all
  SourcePackage: eclipse
  UpgradeStatus: No upgrade log present (probably fresh install)

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