There have been a few posts regarding transparency under Linux. I have put that code together so that it can be used directly. This works for me:

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public def osName = FX.getProperty( "javafx.os.name" );
public def IS_LINUX = osName.contains( "inux" );
public def IS_MAC = osName.contains( "mac" );
public def IS_WINDOWS = osName.contains( "indows" );
public def IS_SOLARIS = osName.contains( "olaris" );

/**
 * Is the version of the running JDK at least major.minor.micro_update?
 * In 1.6.0_18 macro=1,minor=6,micro=0,update=18
 */
public function jdkAtLeast( macro: Integer, minor: Integer, micro: Integer, update: Integer ): Boolean {
  def runtimeVersion = java.lang.System.getProperty( "java.runtime.version" );  
  def pattern = java.util.regex.Pattern.compile( "^(\\d)\\.(\\d)\\.(\\d)_(\\d+)-" );
  def matcher = pattern.matcher( runtimeVersion );
  if ( matcher.find() ) {
    def currentMacro = Integer.valueOf( matcher.group( 1 ) );
    def currentMinor = Integer.valueOf( matcher.group( 2 ) );
    def currentMicro = Integer.valueOf( matcher.group( 3 ) );
    def currentUpdate = Integer.valueOf( matcher.group( 4 ) );
    if ( currentMacro < macro or currentMinor < minor or currentMicro < micro or currentUpdate < update ) {
      return false;
    }
    }
  true
  }

public function fixTransparency() {
  if ( IS_LINUX and jdkAtLeast( 1, 6, 0, 14 ) ) {
    java.lang.System.setProperty( "javafx.allowTransparentStage", "true" );
  }
}