Why is that? If your reaction time is about the same to both sounds and you're standing an equal distance away from both the catcher and 2B, wouldn't the stopwatch give a pretty fair reading?
I got the chance to watch Jenny Topping do a few throwdowns this past weekend. "Wow" is all I can say. She's obviously got a rifle for an arm, but the pinpoint accuracy of those throws was what truly amazed me.
It is only useful for you to compare catchers under a controlled situation. It is not useful for us to compare my catchers to your catchers since how I use the stopwatch and my conditions will vary from your use and conditions.
I have seen this quite often at camps/showcases with multiple coaches timing pop times and home to first. Variances of up to .5 seconds which is huge are not uncommon. I have found that if you do it under game conditions and use video the results can be quite humbling.