Letters to a novice programmer

Dear novice, this time it has been a short while, isn't it? When you have a dll that you call from both a Java app and C++ app with the same inputs but the outputs differ, do not suspect that there might be something wrong with the operating system or JNI. Your problems will always be due to something you did wrong.

You should write some debug code inside the C++ dll that prints dll inputs to a file. Run the dll from Java and C++ and compare dll inputs. I guarantee you that you will see a difference there because most probably you did something wrong before passing the inputs to dll like using a wrong index or making an erroneous unit conversion.

Another tip: When comparing files, never trust your eyes, always use a comparison tool like Total Commander's "Compare by content" or Beyond Compare.