Works fine here. Since the window manager handles window decorations, you might want to tell us about your setup.

I installed everything with pacman -S eclipse from a bare linux install. Maybe something is missing.

I have fluxbox as windowmanager, use the radeon driver,
java -version:
java version "1.7.0_55"
OpenJDK Runtime Environment (IcedTea 2.4.7) (ArchLinux build 7.u55_2.4.7-1-x86_64)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)

Tried with a blank linux user and .xinitrc to avoid any user config issues
#!/bin/bash
setterm -blank 0
xset s off
xset -dpms
startfluxbox & wmpid=$!
wait $wmpid

Then start eclipse, shows red square icon.

Then I also tried to make a Java program that displays a frame with icon. But this works OK, it displays icon!
import javax.swing.*;
import java.awt.*;
public class JB
{
public JB()
{
JFrame frame = new JFrame("FrameDemo");
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
//tried some other sizes of eclipse.png found also works ok
//such as /usr/share/icons/hicolor/16x16/apps/eclipse.png
ImageIcon img = new ImageIcon("/usr/share/eclipse/plugins/org.eclipse.epp.package.standard_2.0.2.20140224-0000/eclipse32.gif");
frame.setIconImage(img.getImage());
frame.pack();
frame.setVisible(true);

}
public static void main(String [] args)
{
new JB();
}
}

no problems with KDE, eclipse and radeon driver,

maybe it's a bug in fluxbox, check your fluxbox configuration :

https://wiki.archlinux.org/index.php/Fluxbox

see also systems log ( dmesg, Xorg.o.log ) if you can find a clue

Ok, I tried with kde, and the icon works there.

When I installed kdebase it added 166 packages and 1 Gb.
But even though it worked in kde, it still did not work when going back to fluxbox. So those packages did not help for fluxbox.

It also happens with xf86-video-vesa video driver.

So it seems to be something with fluxbox. But all other apps have icons in fluxbox.

The icon now works with Eclipse Luna.
So I guess this can be closed now.