FileAppender writes the Header again when an existing LogFile exists.
FileAppender should write the header only once per file (functionality not
documented). If so, the method writeHeader should check whether the file is
empty before writing a new header. If the file already contains data, no header
should be written. Otherwise you could end up having multiple headers in your
file (if you restart your JVM several times for instance).

A fix could look like this:

protected void writeHeader() {
	File logFile = new File(getFile());
	if (layout != null && this.qw != null && logFile.length() == 0) {
		this.qw.write("my Header\n");
	}
}