Robert the author of jamvm has been assisting me with this and he has managed find another error message, which does give a good clue as to what the problem is.
I am using RXTXcomm package, which of course on my dev. system works because there are supported libraries, however on the Yun I don't think they're are.
So I will probably need to roll my own native library and JNI package to provide the serial interfacing.