Serial requires more than just jemplode.jar to work properly. In fact it requires native code to do its thing (which gets installed as part of the jEmplode installer on Windows). If you take your 45 install and replace the jar file with 54's, I think it should work (though you just won't have the most recently VM ... though you could actually try replacing the JRE in the installer folder with a newer one -- no promises that will work, but it might).
Actually, you say "both jemplodes can see it" -- do you mean the .jar launched one can too? That would really surprise me if that's true.
And yes, it's a known isue that jEmplode does not support 1.0 firmwares. A known and will-never-be-fixed issue.
ms