We are 100% POSIX compliant.
If the Java application is coded so it can talk with the built-in COM port (/dev/ttyS0), then that code will work perfectly against the RealPort devices as well.
One possibility that comes to mind is that maybe the application doesn't like the device naming convention of the Realport devices. This would be a change necessary in the application though, not the driver. One possibility that might work if thats the case would be creating symbolic links to the Realport devices with a name acceptable to the application(ttyS4... or whatever the first open device name would be). Rather than recoding the application, this would be a workaround.
You'll want to check deeper into the javax.comm extension documentation to see if this is the case. If you need further assistance with this, I'd recommend calling in to Technical Support so we can get a case created and begin documenting this issue.