Probably what type on DS you use and if you have an external timer with milisecond display; besides, you haven't been asked yet what you actually mean with "don't hit the seed". When you calibrate your results, do you manage to get your desired actual seconds? The results in the time finder is the time the game should start - which means you probably have to press A on the home screen a bit earlier, depending on your calibration results.
If that is not a problem, then you probably have got another Timer0 (again, find it out by calibrating). In that case, use an external timer, recalibrate your game, find out your most common Timer0 and pray for the correct results in the future.