This week's book giveaway is in the OCMJEA forum. We're giving away four copies of OCM Java EE 6 Enterprise Architect Exam Guide and have Paul Allen & Joseph Bambara on-line! See this thread for details.
I think JTextArea uses a newline character to separate lines. So if you're on an OS that uses a different line separator (like Windows) you'd need to adapt that when saving to a file. Inserting a carriage return character before each newline character might do the trick.