Have you the Mega and the Uno connected at the same time?
I haven't used Windows for years so forgive me if this does not apply ....
If you only have the Uno connected and communicating with the Java code and then plug out the Uno and replace it with the Mega will the PC see it attached to the same port so that the same Java code will work?
I'm pretty sure I have communciated with an Uno and Mega using JSSC (I'm using JRuby on Ubuntu).
...R