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Java appending to text file working differently on another system?

When I run the below on a windows machine it works as expected, appending to the end of the text file on a new line, however when run in a jail on my FREENAS server inputs will simply append to the last line and never make a new line. Has anyone experienced this?
BufferedWriter writer = new BufferedWriter(new FileWriter(filename,true));
writer.newLine();
writer.append(desired);
writer.close();

Despite the textfile looking like this after being given input on Windows:
cat
dog
mouse
and on FREENAS the textfile looking like this:
catdogmouse
They are both treated the same by Java and when read in with:
String line = Scanner.nextLine();
System.out.println(line);
Both produce:
cat
dog
mouse

How can I write UTF-8 chars on java application?

I want to write
ısı
to csv on java netbeans. It works fine when I debug the code. But when I clean and build the project, I run .jar application and then when I look the csv I see
?s?
How can I solve this ?
thanks in advance.
EDIT
I use this to write :
PrintWriter csvWriter = new PrintWriter(new File("myfile.csv")) ;
csvWriter.println("ısı") ;

With this code:
PrintWriter csvWriter = new PrintWriter(new File("myfile.csv")) ;
csvWriter.println("ısı") ;
you are using the default character encoding of your system, which may or may not be UTF-8. If you want to use UTF-8, you have to specify that:
PrintWriter csvWriter = new PrintWriter(new File("myfile.csv"), "UTF-8");
Note that even if you do this, you might still see unexpected output. If that's the case, then you will need to check if whatever program you use to display the output (the Windows command prompt, or a text editor, or ...) understands that the file is in UTF-8 and displays it correctly.

Format of the output

I am using eclipse to run my program. My programs gives 1000 lines as output, and I write the output on a text file successfully. The problem is that the output on the text file is not same as on the console. On the console there are separate lines, but on text file all lines are appended as one line.
How to get the same console format in a text file?

You will have to make sure of the following:
When writing a line to a file you are including a line separator character(s), you can get a platform independent line separator using the following
System.getProperty("line.separator");
When viewing the text file, some app's (like notepad) may not display new line characters the same as others
The app you are using to view the file will need to be set to view in a monospaced font (such as Courier New)

completely guessing what you are doing but i think you need to do this.
BufferedWriter bw = new BufferedWriter(new FileWriter(f, false));
while ( rs.next() ) {
// code to write a line.
bw.write("\r\n");
}
use
bw.write("\r\n");
instead of
bw.newLine();
This is for windows systems POSIX systems do newlines differently i believe.
\n is a new line operator just remember that.

Well if you are using a PrintWriter I would simply do
PrintWriter pw = new PrintWriter(file);
while(...you still have data){
pw.println(<yourString>);
}
you can also append the string "\n" to create a new line manually

"\n" not working when exported to .jar file

I have an output file for a program I have written. It is written by a FileWriter and BufferedWriter.
FileWriter errout = new FileWriter(new File("_ErrorList.txt"));
BufferedWriter out = new BufferedWriter(errout);
Later I write to the file using lines similar to.
out.write("Product id:" + idin + " did not fetch any pictures.\n ");
When I simpily run the program in Eclipse, the output file is formatted correctly, with each message being written on a new line. However when I export to a .jar file, it no longer works and puts every message on a single line, as if the "\n" was not working.
Am I using the FileWriter/BufferedWriter incorrectly, or does it not work in a .jar file?

You should not use '\n' directly. Either use out.newLine() to introduce a line break, or wrap the BufferedWriter into a PrintWriter, and use out.println().
This has nothing to do with the .jar file, anyway. More likely is Eclipse being clever and showing you line breaks, while the operating system does not.

One, check that the line separator is valid. Use System.getProperty("line.separator") as provided by #Andrew Thompson.
Another option if you're doing a lot of this writing new lines is to wrap your BufferedWriter in a PrintWriter.
FileWriter errout = new FileWriter(new File("_ErrorList.txt"));
BufferedWriter out = new BufferedWriter(errout);
PrintWriter printWriter = new PrintWriter(out);
printWriter.println("Product id:" + idin + " did not fetch any pictures.");

Inserting New Lines when Writing to a Text File in Java

I have a slight delema with learning FileWriter... The ultimate goal is writing a program that will "spawn" a .bat file that will be executed by the batch code that launched the .jar. The problem is, I have no clue how to make sure that every FileWriter.write(); will print on a new line... Any ideas??

To create new lines, simply append a newline character to the end of the string:
FileWriter writer = ...
writer.write("The line\n");
Also, the PrintWriter class provides methods which automatically append newline characters for you (edit: it will also automatically use the correct newline string for your OS):
PrintWriter writer = ...
writer.println("The line");

Use a BufferedWriter and use writer.newLine() after every write-operation that represents one line.
Or, use a PrintWriter and writer.println().

If you are using BufferedWriter then you can use an inbuilt method :
BufferedWriter writer = Files.newBufferedWriter(output, charset);
writer.newLine();