BHPS,
JAR FCL defines flight time for FCL purposes ONLY. Flight and Duty Time limitations (for commercial operations) are governed by NON JAR requirements. Even in JAR-OPS3, the FDTL section is blank because (I understand) that the committee couldn't reach any agreement.
Each operator still has to "define" its own scheme and definitions by using the CAA publication (CAP 372) which is unchanged (for now).
Of course the JAA has now been rather subverted by the appearance on the scene of the European Aviation Safety Agency (EASA) courtesy of the EU. At present, it only seems to consist of a website and a new CEO - a French ex-army Colonel !! Who knows what will happen with yet another lot of regulators..............