FULL PRODUCT VERSION :
initial tests on ...
java version " 1.7.0_17 "
Java(TM) SE Runtime Environment (build 1.7.0_17-b02)
Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)

same results on ...
java version " 1.8.0-ea "
Java(TM) SE Runtime Environment (build 1.8.0-ea-b80)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b21, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Mac OS X Lion 10.7.5 (11G63)
Darwin Lux.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64

Mac OS X 10.8.2 (12C60)
Darwin eV.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64

EXTRA RELEVANT SYSTEM CONFIGURATION :
Use Netbeans 7.3 beta and Netbeans 7.3 general release.

Tested with same results on three machines: MacBook Pro and two different Mac Minis.

A DESCRIPTION OF THE PROBLEM :
A. extraneous files are create in /User/~/Library/Preferences such as ...

806ac122-aea4-41c6-8760-2fc846a5b2d2.child_node_a.child_node_b.plist.lockfile
806ac122-aea4-41c6-8760-2fc846a5b2d2.child_node_a.child_node_b.plist

B. removing the preference nodes, flush() and sync() leave residual files in the Preferences folder.

C. sometimes... Netbeans debugger will crash when stepping through the preferences junit test.

A & B always happen.
C. sometimes happens.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the attached JUnit test.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
1. preference node paths to be contained in com.apple.java.util.prefs.plist

2. preference node paths to be cleanly removed.
ACTUAL -
A. extraneous files are create in /User/~/Library/Preferences such as ...

806ac122-aea4-41c6-8760-2fc846a5b2d2.child_node_a.child_node_b.plist.lockfile
806ac122-aea4-41c6-8760-2fc846a5b2d2.child_node_a.child_node_b.plist

B. removing the preference nodes, flush() and sync() leave residual files in the Preferences folder.

C. sometimes... Netbeans debugger will crash when stepping through the preferences junit test.

A & B always happen.
C. sometimes happens.

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
import java.util.UUID;
import java.util.prefs.BackingStoreException;
import java.util.prefs.Preferences;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.junit.Assert.*;

/**
 *
 * @author marc
 */
public class PreferencesTest {

    private String uuidStr;
    private Preferences testPrefs;

    public PreferencesTest() {
    }

    @BeforeClass
    public static void setUpClass() {
    }

    @AfterClass
    public static void tearDownClass() {
    }

    @Before
    public void setUp() throws BackingStoreException {
        uuidStr = UUID.randomUUID().toString();
        testPrefs = Preferences.userRoot().node(uuidStr);
        testPrefs.flush();
    }

    @After
    public void tearDown() throws BackingStoreException {
        testPrefs.removeNode(); // remove node and all descendants
        testPrefs.flush();
    }

    @Test
    public void hello() throws BackingStoreException {
        System.out.println( " ... Hello ... " );
        System.out.println( " ABSOLUTE PATH: " + testPrefs.absolutePath());

        // create relative child node abc
        Preferences childNodeABC = testPrefs.node( " CHILD_NODE_A/CHILD_NODE_B/CHILD_NODE_C " );
        String valueAbcUuid = UUID.randomUUID().toString();
        childNodeABC.put( " KEY_C " , valueAbcUuid);
        childNodeABC.flush();

        assertEquals(valueAbcUuid, childNodeABC.get( " KEY_C " , " NOT_FOUND " ));
        
        // create relative child node XYZ
        Preferences childNodeXYZ = childNodeABC.node( " CHILD_NODE_PART_X;PART_Y;PART_Z " );
        String valueXyzUuid = UUID.randomUUID().toString();
        childNodeXYZ.put( " KEY_Z " , valueXyzUuid);
        childNodeXYZ.flush();
        
        assertEquals(valueXyzUuid, childNodeXYZ.get( " KEY_Z " , " NOT_FOUND " ));

        childNodeABC.removeNode();
        testPrefs.sync();
    }
}

---------- END SOURCE ----------