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Well, there is always the chance that Java is inlining your method for you. e.g., it notices that your method is only a line long and therefore just places it inside your main loop instead of making the call.
In fact you might want to place each of the loops into it's own program since there is a chance if Java is using the Hot Spot compiler it will have optimized the 2nd loop because of the 1st loop...
Also, which Java version and operating system are you using? Some of the earlier Java versions don't handle timing very well. I think they fixed the timing issues with Java 1.5.
Sorry if this is rambling a bit much but it is late and I'm might not be thinking completely straight.
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