Going back to Malcolm's original comments, I agree that the mistake was to rely on an unproven (TT - wise, that is with the start intervals) system.
With the good old 20/20 hindsight, maybe the original, proven system should have been retained and a random selection of riders picked out to test the transponder system, (at the organiser's cost, of course!). This can still be done at the MGP but it is unfair on the riders who have already parted with their hard earned cash for the transponders.
The electronic system can be highly accurate but I fear many people will have lost confidence already due to the poor performance. Properly set up, the results should be instantaneous and available to all.