With Merlin builds 45 and 46, the following boiled-down test case shows the wrong result for a "long" subtraction operation:

public class TestBug {
    public static void main(String[] args) {
        int reps = Integer.parseInt(args[0]);

        long start = 1; // System.currentTimeMillis();
        System.out.println("start = " + start);

        for (int i = 0; i < reps; i++) {
            //
        }

        long end = 2; // System.currentTimeMillis();
        System.out.println("end = " + end);

        long delta = end - start;
        System.out.println("delta = " + delta);
    }
}

[terrier] 77 % java -version
java version "1.4.0-beta"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.0-beta-b46)
Java HotSpot(TM) Client VM (build 1.4beta-B45, mixed mode)
[terrier] 78 % java TestBug 13999
start = 1
end = 2
delta = -4294967294

The result of "end - start" should obviously be 1, but the calculated result is way off.

Note that if the command line argument is less than 13999, or if the "-Xint" option is used (interpreter only), then this test case succeeds.