Different results of Text Maker in windows and unix

The class AbstractApplyScriptHandlerJob when called from the workbenck calls, for reding text to be analyzed the method:
org.apache.uima.pear.util.FileUtil.loadTextFile(new File(each), "UTF-8");
Such a method return nelines in window as 2 new lines. Therefore basic TextMarker annotations appears like:
line BREAK BREAK
line BREAK BREAK
Therefore grammars written on windows must take into account the double break which make them not applicable when running on unix or when using other read methods, such as:
Scanner sc = new Scanner(inFile, "UTF-8");
String out = "";
while (sc.hasNextLine())

{ out += sc.nextLine() + "\n"; }

Relates to:
https://issues.apache.org/jira/browse/UIMA-2133t