If it works in Eclipse testing the .class file, but does not work from a jar file, you probably have a standard class/library not found issue.
( not directly related to RxTx or Processing or Arduino )
What makes it perhaps harder than usual here, is the required native library, which has to be found and must be for the desired environment ( 32 / 64 bit )
won’t even return a exception message:
Native libraries can crash the JVM ! That produces an error message (and file) on a different level 
Before testing the your jar file:
Do you get the class file to execute outside Eclipse ? This shows if you have control over the required environment.
.class to .jar adds another level of possible problems.
A bit more information about your environment, what happens, and what you expect, might help us give you more hints 8)
getPortIdentifiers() does not need many lines of code to be in a suitable environment, can you post them here ?