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As a quick (and dirty) work-around, one can change the code so that the following is used for replacements:
[[section]]{{key}}

This should be enough for regexp.

Class: JFigParser
Methode: getRegexSubstitution

protected static Pattern getRegexSubstitution() throws JFigException {
if (regexSubstitution == null) {
// ? sets to non-greedy. \\) says look for literal ")"
regexSubstitution = Pattern.compile("(.*)(\\" + JFigConstants.SECTION_START_DELIMITER + "\\"+JFigConstants.SECTION_START_DELIMITER+")(.*?)(\\" +
JFigConstants.SECTION_END_DELIMITER+"\\"+JFigConstants.SECTION_END_DELIMITER+"?\\" + // 0 or 1 end section delimiter
JFigConstants.KEY_START_DELIMITER+"\\"+JFigConstants.KEY_START_DELIMITER + ")(.*?)(\\" + JFigConstants.KEY_END_DELIMITER +"\\" + JFigConstants.KEY_END_DELIMITER +
")(.*?)$", Pattern.MULTILINE);
}

return regexSubstitution;

}

Stefaan