I have found out a workaround. It seems to be a bug in SWT. So not related to 
Java, but actually Eclipse UI stack.
The workaround is to export the following environment variable before launching 
the application :
export GDK_NATIVE_WINDOWS=1

The bug is well explained in this blog post:
http://blog.export.be/2009/10/fixing-eclipse-for-ubuntu-karmic-
koala-9-10/

I will update the bug report so it reflects the real problem.

N.B. Eclipse corrected the bug and it will be fixed for Eclispe 3.6.
As for Azureus/Vuze, the bug will be there as long as they do not upgrade to 
Eclipse 3.6 (not yet released!)... As i'm not using it, I'm rather lazy to 
subscribe to their forums (http://forum.vuze.com/forum.jspa?forumID=4) or bug 
report system (https://jira.vuze.com/secure/Dashboard.jspa) to tell them about 
the bug.

** Bug watch added: Eclipse bugs #287307
   https://bugs.eclipse.org/bugs/show_bug.cgi?id=287307

** Also affects: eclipse via
   https://bugs.eclipse.org/bugs/show_bug.cgi?id=287307
   Importance: Unknown
       Status: Unknown

** Summary changed:

- Java UI bug: cannot click button
+ SWT UI bug with GTK on Karmic: cannot click button

** Changed in: sun-java6 (Ubuntu)
       Status: New => Invalid

** Tags added: eclipse swt
** Tags removed: java

** Description changed:

- I am developing application using Eclipse CDT (C++) and Eclipse EMF
- (Java/Eclipse RCP). However, in both IDE it is really unpleasant since I
- upgrade to Karmic to develop because sometimes you cannot click a button
- in the Java UI! I really says sometimes because, some button are
- clickable, some others are not.
+ Updated information : this seems to be an SWT (Eclipse UI framework)
+ bug, not Java related.
+ 
+ Original bug report:
+ I am developing application using Eclipse CDT (C++) and Eclipse EMF 
(Java/Eclipse RCP). However, in both IDE it is really unpleasant since I 
upgrade to Karmic to develop because sometimes you cannot click a button in the 
Java UI! I really says sometimes because, some button are clickable, some 
others are not.
  
  Behaviour:
  You press the left mouse button on a Java UI button, you see it as being 
pressed, and once you release the pressure on the mouse, you see the Java UI 
button as unpressed (it usually gains the "focus") however nothing happen. But, 
as it gains the "focus", you can press the space bar to actually "really" press 
the button and then it works. However, this is not the expected behaviour.
  
  Impacted package:
-  - sun-java6-jdk/jre
-  - openjdk
-  - and even Sun own version downloaded from their websites (including latest 
JDK 6 u18)
+  - sun-java6-jdk/jre
+  - openjdk
+  - and even Sun own version downloaded from their websites (including latest 
JDK 6 u18)
  
  Note: this is a regression in comparison to Jaunty.
  
  ProblemType: Bug
  Architecture: i386
  Date: Sat Feb 20 11:11:47 2010
  DistroRelease: Ubuntu 9.10
  Package: sun-java6-jdk 6-15-1
  ProcEnviron:
-  LANGUAGE=en_GB.UTF-8
-  PATH=(custom, user)
-  LANG=en_GB.UTF-8
-  SHELL=/bin/bash
+  LANGUAGE=en_GB.UTF-8
+  PATH=(custom, user)
+  LANG=en_GB.UTF-8
+  SHELL=/bin/bash
  ProcVersionSignature: Ubuntu 2.6.31-19.56-generic-pae
  SourcePackage: sun-java6
  Uname: Linux 2.6.31-19-generic-pae i686
  XsessionErrors:
-  (gnome-settings-daemon:2388): GLib-CRITICAL **: g_propagate_error: assertion 
`src != NULL' failed
-  (nautilus:2481): Eel-CRITICAL **: eel_preferences_get_boolean: assertion 
`preferences_is_initialized ()' failed
-  (polkit-gnome-authentication-agent-1:2498): GLib-CRITICAL **: 
g_once_init_leave: assertion `initialization_value != 0' failed
-  (gnome-panel:2480): Gdk-WARNING **: 
/build/buildd/gtk+2.0-2.18.3/gdk/x11/gdkdrawable-x11.c:952 drawable is not a 
pixmap or window
+  (gnome-settings-daemon:2388): GLib-CRITICAL **: g_propagate_error: assertion 
`src != NULL' failed
+  (nautilus:2481): Eel-CRITICAL **: eel_preferences_get_boolean: assertion 
`preferences_is_initialized ()' failed
+  (polkit-gnome-authentication-agent-1:2498): GLib-CRITICAL **: 
g_once_init_leave: assertion `initialization_value != 0' failed
+  (gnome-panel:2480): Gdk-WARNING **: 
/build/buildd/gtk+2.0-2.18.3/gdk/x11/gdkdrawable-x11.c:952 drawable is not a 
pixmap or window

-- 
SWT UI bug with GTK on Karmic: cannot click button
https://bugs.launchpad.net/bugs/524929
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