FULL PRODUCT VERSION :
java version "1.6.0-beta2"
Java(TM) SE Runtime Environment (build 1.6.0-beta2-b86)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0-beta2-b86, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Linux kowloon 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux

A DESCRIPTION OF THE PROBLEM :
System.nanoTime() is returning values which don't agree with what System.currentTimeMillis().

The bug was found on Linux AS4 on an Opteron processor, running the Java 1.6 beta 2 JVM (64-bit). The problem does not exist if I use the Java 1.5 32-bit JVM on the same machine.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the sample code below, as follows (output from console on the Linux host 'kowloon'):

kowloon% uname -a
Linux kowloon 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux

kowloon% cat Test.java
import java.lang.*;
import java.util.*;

public class Test
{
    public static void main(String args[])
    {
        System.err.println("nanoTime = " + System.nanoTime());
        System.err.println("milliTime = " + System.currentTimeMillis());
    }
}

kowloon% /usr/jdk1.6.0/bin/javac Test.java

kowloon% /usr/jdk1.6.0/bin/java Test
nanoTime = 14112906333480828
milliTime = 1159561880925

kowloon% /usr/jdk1.5.0_02/bin/javac Test.java

kowloon% /usr/jdk1.5.0_02/bin/java Test
nanoTime = 1159561909537191000
milliTime = 1159561909537

kowloon% /usr/jdk1.6.0/bin/java -version
java version "1.6.0-beta2"
Java(TM) SE Runtime Environment (build 1.6.0-beta2-b86)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0-beta2-b86, mixed mode)

kowloon% /usr/jdk1.5.0_02/bin/java -version
java version "1.5.0_02"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_02-b09)
Java HotSpot(TM) Server VM (build 1.5.0_02-b09, mixed mode)

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
System.nanoTime() should return a value approximately equal to System.currentTimeMillis() * 1000
ACTUAL -
Return value did not resemble System.currentTimemillis().

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
import java.lang.*;
import java.util.*;

public class Test
{
    public static void main(String args[])
    {
        System.err.println("nanoTime = " + System.nanoTime());
        System.err.println("milliTime = " + System.currentTimeMillis());
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Use System.currentTimeMillis() * 1000 whenever nanoTime is required. This of course causes a great loss in precision.