We make use of a java application that manages a pinpad via the serial port. This works perfectly on windows with the Sun Comm.jar, the supplied dll and the properties file.
I know this is an old question but I have created a Java package and native library to allow serial port read and write, currently in synchronous mode only.
It's open source and available on GitHub:
j232 - The Java source code
libj232 - j232's native library.
The wiki page is here.
Note this is a Linux only package and library.