First, some corrections:
The number of bytes that make up a character is not fixed; it depends on the encoding that's being used to convert between bytes and characters. (Read this
.) You're probably thinking of the way Java strings are stored; they use the UTF-16
encoding, which uses two bytes per character (usually--see the article), but that has nothing to do with how the text is stored on disk.
It used to be the case that Macs favored the carriage-return ('\r' or '\u000D') for line separators, but as of version 10 (OSX), Mac OS is based on Linux, which prefers the linefeed ('\n' or '\u000A').
However, it doesn't matter that much what the operating system
thinks a line separator should be, because it's the application
(in this case, your Java program) that has to read and write the files. Virtually every modern application will accept any of the three major styles of line separator ("\n", "\r", or "\r\n"). BufferedReader is no exception; you can use a different separator at the end of every line, and BufferedReader will handle them correctly.
There is, unfortunately, one very important exception: Windows Notepad. It refuses to recognize anything except the DOS/Windows-style carriage-return+linefeed ("\r\n") line separator. If it encounters a linefeed or carriage-return by itself, Notepad renders it as a rectangle instead of a line break. That's probably not the cause of your problem, since you're using a Mac, but it's useful to know about (not to mention infuriating).
Now that all that's out of the way, we'll need some more info before we can help you. Like, how exactly are you reading and writing the files? What's the exact code you use to construct the Reader and Writer? How do you write the line separators? Do you use BufferedWriter#newLine(), or do you explicitly write a "\r"? And how do you view the contents of the files?