The change to the definition of flight time JAR-FCL was to bring it into line with ICAO Annex 6 Part III. The ICAO change was undertaken to remove the complexity of the previous definition with its accompanying notes (the definition is clearer but the application is now more complex).
The responsibility for JAR-OPS 1/3 Subpart Q was taken away from the JAA by the EU several years ago - there was no question of the committee agreeing or not agreeing DGTREN (the commission transport group) declared itself competant on the issue. The EU, having failed in its exercise to achieve consensus on Flight and Duty Times regulations, is now attempting to hand it back to the JAA (looks like a poisoned chalice).
There is considerable opposition to the new definition of Flight Time in ICAO Annex 6 but as the NAAs appear to be split 50:50 for and against, it is likely that the definition will remain and notes will be added to make the intent clearer.
212man is correct in his statement that the new definition will reduce the number of hours a pilot can fly as the run-up and run-down time will be added to the total.