From
Sun's Site
Note: The GTK+ look and feel was released in all versions of the 1.4.2 SDK. However, it was not included in the 1.4.2 JRE release for Microsoft Windows. If you are running the 1.4.2 JRE for Windows and wish to use the GTK+ look and feel, you need to download the 1.4.2 SDK. We expect GTK+ to be shipped for all platforms in future JRE releases.
Could it be that you are using the JRE's java.exe to run the app outside of eclipse instead of the JDK's java.exe?