FULL PRODUCT VERSION :
C:\Users\Jim>java -version
java version "1.6.0_29"
Java(TM) SE Runtime Environment (build 1.6.0_29-b11)
Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Windows 7 6.1, Java SE 6 Update 29

A DESCRIPTION OF THE PROBLEM :
If both 32-bit and 64-bit Java programs are installed on a Windows 7 64-bit system, the Preferences API uses two different locations to store preferences values:

Under the 64-bit JVM:
HKEY_LOCAL_MACHINE\Software\Javasoft\Prefs
Under the 32-bit JVM:
HKEY_LOCAL_MACHINE\Software\Wow6432Node\Javasoft\Prefs
This means that programs running under the 32-bit Nebeans IDE behave differently than programs running in the default 64-bit environment outside the IDE.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
On 64-bit Win 7, with 64-bit Java installed...
1) Create a program that writes a system Preferences value.
2) Create a command prompt window with admin privs
3) From command window, invoke java program created in step 1 above to set preferences value
4) Create program to read preference value.
5) Run program from a non-privileged command line, it will successfully retrieve value set in step #3
6) Run program from step #4 from within Netbeans IDE. It will fail to read the value from step #3.



EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
I would expect the Preferences API to work consistently over both 32-bit and 64-bit Java.
ACTUAL -
Prefrences set with the 32-bit JVM can only be read by applications running with the 32-bit JVM. Values set with the 64-bit JVM can only be read by the 64-bit JVM.

ERROR MESSAGES/STACK TRACES THAT OCCUR :
Logged by Netbeans IDE in response by attempt to read preference value that was set by external program running as admin:

WARNING: Could not create windows registry node Software\JavaSoft\Prefs\prefsexample at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
Jan 16, 2012 4:40:10 PM java.util.prefs.WindowsPreferences WindowsRegOpenKey1
WARNING: Trying to recreate Windows registry node Software\JavaSoft\Prefs\prefsexample at root 0x80000002.
Jan 16, 2012 4:40:10 PM java.util.prefs.WindowsPreferences openKey
WARNING: Could not open windows registry node Software\JavaSoft\Prefs\prefsexample at root 0x80000002. Windows RegOpenKey(...) returned error code 2.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------

public class MyPreferences {
     Preferences prefs = Preferences.systemNodeForPackage (getClass ());
       
     void putValue(String key, String val) {
         prefs.put(key, val);
     }
     String getValue(String key) {
         String result = prefs.get(key, null);
         return result;
     }
}
public class PrefReader {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        MyPreferences myPrefs = new MyPreferences();
        String resultString = myPrefs.getValue("TEST");
        System.out.println("The result is: "+resultString);
    }
}

public class PrefWriter {

    public static void main(String[] args) {
        // TODO code application logic here
        MyPreferences myPrefs = new MyPreferences();
        myPrefs.putValue("TEST", "This is a test");
        System.out.println("TEST is now updated.");
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Invoke the netbeans IDE with admin privs, and run the set value programs from within the IDE to create a duplicate set of preferences values (or change the path to use 32-bit JVM).