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.
It's been a while since I've done this. I remember that you can't just open /dev/ttyS0 as a file and I/O to it.
I remember having the same problem with Sun IO jars also.
The solution I remember settling on was to create a small command-line program in C that echoed stdin to the serial port and serial port in to stdout. Then, I launched this program from my java process. I don't have the code but there are lots of examples on the web for c programs that write to linux serial ports.
We've been using the SerialIO libraries for Java serial communications on both Windows and Linux for several years now with great results (and no, I don't work for them :-)):
http://serialio.com/products/serialport/serialport.php
The libraries do not autodetect the available serial ports on Linux though - you have to manually configure them.
We did not change much, nothing in the libraries used. but removing the use of an EventListener on the serial port object fixed the problem.
This actually allowed for our code to work on linux (jre1.4.2, slackware and Suns Comm3 drivers) where this was not a problem on windows - strange.
Phill
Make sure that you are using a user with permissions to access the serial ports. Some distributions put the serial ports in the uucp group, so make sure that the user belongs to that group.
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.