FULL PRODUCT VERSION :
java version "1.5.0_04"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_04-b05)
Java HotSpot(TM) Client VM (build 1.5.0_04-b05, mixed mode, sharing)

and

java version "1.5.0_04"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_04-b05)
Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_04-b05, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
Linux linux 2.6.12.5 #3 Sat Aug 20 10:27:33 PDT 2005 x86_64 unknown unknown GNU/Linux

(I reported as a general Linux (not only 64bit) because e17 developers did apply a patch to "emulate" e16 to make jvm work there)

EXTRA RELEVANT SYSTEM CONFIGURATION :
tested for applets, java awt apps, java Swing apps and java console apps with server and client configuration

e17 was compilled as a 64bit app and both modes (64bit and 32bit) jvm were tested

A DESCRIPTION OF THE PROBLEM :
when trying to run any java app using JVM 1.4 or 1.5 it fails with the following error:

Atom was 0
java.lang.ExceptionInInitializerError
        at org.netbeans.core.NonGui.getUserDir(NonGui.java:118)
        at org.netbeans.core.NonGui.getLogDir(NonGui.java:147)
        at org.netbeans.core.CLIOptions.initialize(CLIOptions.java:192)
        at org.netbeans.core.Main.start(Main.java:304)
        at org.netbeans.core.TopThreadGroup.run(TopThreadGroup.java:90)
        at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException: Failed to retrieve atom name.
        at sun.awt.X11.XlibWrapper.XGetAtomName(Native Method)
        at sun.awt.X11.XAtom.<init>(XAtom.java:219)
        at sun.awt.X11.XAtom.get(XAtom.java:146)
        at sun.awt.X11.XAtom.getAtomListProperty(XAtom.java:630)
        at sun.awt.X11.XAtom.getAtomListPropertyList(XAtom.java:644)
        at sun.awt.X11.XProtocol.checkProtocol(XProtocol.java:37)
        at sun.awt.X11.XNETProtocol.doStateProtocol(XNETProtocol.java:273)
        at sun.awt.X11.XWM.initializeProtocols(XWM.java:1178)
        at sun.awt.X11.XWM.<init>(XWM.java:113)
        at sun.awt.X11.XWM.getWM(XWM.java:559)
        at sun.awt.X11.XWM.init(XWM.java:1169)
        at sun.awt.X11.XToolkit.<init>(XToolkit.java:320)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
        at java.lang.Class.newInstance0(Class.java:350)
        at java.lang.Class.newInstance(Class.java:303)
        at java.awt.Toolkit$2.run(Toolkit.java:833)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:804)
        at javax.swing.UIManager.initialize(UIManager.java:1262)
        at javax.swing.UIManager.maybeInitialize(UIManager.java:1245)
        at javax.swing.UIManager.getDefaults(UIManager.java:556)
        at javax.swing.filechooser.FileSystemView.getFileSystemView(FileSystemView.java:63)
        at org.openide.filesystems.FileUtil.<clinit>(FileUtil.java:49)
        ... 6 more
Atom was 0

I have researched at the source code and i find a little silly the way the JVM try to guess what wm is running, because you are not thinking in another window managers; even some bad positioning happen when using kde in two different pc's; i would recommend to see for more general options inside Xserver and have a default generic config for any other wm (in case it is not registered or a nullpointerException is returned (like in this case)

the window manager should not be relevant when trying to run a Java Console App(some apps of this kind will not run and another ones would run perfectly).


STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
just try to run any java app or applet you want under e17 in a Linux amd64 system.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
run the app (any)
ACTUAL -
Atom was 0
java.lang.ExceptionInInitializerError
        at org.netbeans.core.NonGui.getUserDir(NonGui.java:118)
        at org.netbeans.core.NonGui.getLogDir(NonGui.java:147)
        at org.netbeans.core.CLIOptions.initialize(CLIOptions.java:192)
        at org.netbeans.core.Main.start(Main.java:304)
        at org.netbeans.core.TopThreadGroup.run(TopThreadGroup.java:90)
        at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException: Failed to retrieve atom name.
        at sun.awt.X11.XlibWrapper.XGetAtomName(Native Method)
        at sun.awt.X11.XAtom.<init>(XAtom.java:219)
        at sun.awt.X11.XAtom.get(XAtom.java:146)
        at sun.awt.X11.XAtom.getAtomListProperty(XAtom.java:630)
        at sun.awt.X11.XAtom.getAtomListPropertyList(XAtom.java:644)
        at sun.awt.X11.XProtocol.checkProtocol(XProtocol.java:37)
        at sun.awt.X11.XNETProtocol.doStateProtocol(XNETProtocol.java:273)
        at sun.awt.X11.XWM.initializeProtocols(XWM.java:1178)
        at sun.awt.X11.XWM.<init>(XWM.java:113)
        at sun.awt.X11.XWM.getWM(XWM.java:559)
        at sun.awt.X11.XWM.init(XWM.java:1169)
        at sun.awt.X11.XToolkit.<init>(XToolkit.java:320)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
        at java.lang.Class.newInstance0(Class.java:350)
        at java.lang.Class.newInstance(Class.java:303)
        at java.awt.Toolkit$2.run(Toolkit.java:833)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:804)
        at javax.swing.UIManager.initialize(UIManager.java:1262)
        at javax.swing.UIManager.maybeInitialize(UIManager.java:1245)
        at javax.swing.UIManager.getDefaults(UIManager.java:556)
        at javax.swing.filechooser.FileSystemView.getFileSystemView(FileSystemView.java:63)
        at org.openide.filesystems.FileUtil.<clinit>(FileUtil.java:49)
        ... 6 more
Atom was 0

ERROR MESSAGES/STACK TRACES THAT OCCUR :
Atom was 0
java.lang.ExceptionInInitializerError
        at org.netbeans.core.NonGui.getUserDir(NonGui.java:118)
        at org.netbeans.core.NonGui.getLogDir(NonGui.java:147)
        at org.netbeans.core.CLIOptions.initialize(CLIOptions.java:192)
        at org.netbeans.core.Main.start(Main.java:304)
        at org.netbeans.core.TopThreadGroup.run(TopThreadGroup.java:90)
        at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException: Failed to retrieve atom name.
        at sun.awt.X11.XlibWrapper.XGetAtomName(Native Method)
        at sun.awt.X11.XAtom.<init>(XAtom.java:219)
        at sun.awt.X11.XAtom.get(XAtom.java:146)
        at sun.awt.X11.XAtom.getAtomListProperty(XAtom.java:630)
        at sun.awt.X11.XAtom.getAtomListPropertyList(XAtom.java:644)
        at sun.awt.X11.XProtocol.checkProtocol(XProtocol.java:37)
        at sun.awt.X11.XNETProtocol.doStateProtocol(XNETProtocol.java:273)
        at sun.awt.X11.XWM.initializeProtocols(XWM.java:1178)
        at sun.awt.X11.XWM.<init>(XWM.java:113)
        at sun.awt.X11.XWM.getWM(XWM.java:559)
        at sun.awt.X11.XWM.init(XWM.java:1169)
        at sun.awt.X11.XToolkit.<init>(XToolkit.java:320)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
        at java.lang.Class.newInstance0(Class.java:350)
        at java.lang.Class.newInstance(Class.java:303)
        at java.awt.Toolkit$2.run(Toolkit.java:833)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:804)
        at javax.swing.UIManager.initialize(UIManager.java:1262)
        at javax.swing.UIManager.maybeInitialize(UIManager.java:1245)
        at javax.swing.UIManager.getDefaults(UIManager.java:556)
        at javax.swing.filechooser.FileSystemView.getFileSystemView(FileSystemView.java:63)
        at org.openide.filesystems.FileUtil.<clinit>(FileUtil.java:49)
        ... 6 more
Atom was 0

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
 Frame blah = new Frame("blah");
---------- END SOURCE ----------