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The compiler which comes with the 32-bit JDK and the compiler which comes with the 64-bit JDK is identical. They should also produce identical class files.
What is more likely is that your application cannot find the 64-bit compiler. I vaguely remember that is you configure a random path, it just reutrns null for the compiler (no error) So if you use the reference without checking for null, you will get an NPE.