Setting system properties: difference between "-D" and "System.setProperty"

Hi.
I have a program that relies on the jogl library to display graphics. Internally, jogl loads a native library from disk, with a System.loadLibrary() call. In turn, loadLibrary searches the paths in the system property "java.library.path" to find the jogl DLL/SO files. So, it is my responsibility to ensure that the "java.library.path" property is correctly set.
There are two ways that I know of to set system properties: as an argument to the JRE via the "-D" option and from within an application with the System.setProperty method. However, I have noticed that only the former gives the desired behavior. That is, if I do:
java -Djava.library.path=lib MyProgram{code}
the code in jogl.jar is able to successfully find and load the native libraries in lib/, but if I do:
{code:java}System.setProperty("java.library.path", "lib");{code}
at the beginning of main in my program (before the classes requiring jogl are loaded), I end up with an UnsatisfiedLinkError.
Why does this happen? Why do the 2 methods produce different results? Is specifying native library paths on the command line the only way to ensure that they are found?                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           

See the [System Properties Tutorial|http://java.sun.com/docs/books/tutorial/essential/environment/sysprop.html] section on "Writing System Properties" which says:
Warning: Changing system properties is potentially dangerous and should be done with discretion. Many system properties are not reread after start-up and are there for informational purposes. Changing some properties may have unexpected side-effects.
Also see the [setting java.library.path property in java code|http://forums.sun.com/thread.jspa?threadID=627890] thread in the JNI forum.

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    http://www.sap-img.com/abap/interview-question-on-bapi-rfc-abap-objects-tables.htm
    http://www.sap-img.com/fu033.htm
    http://www.sap-img.com/abap/ale-bapi.htm
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    Re: BAPI and RFC
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