Baseball being what it is, I'm guessing league wide teams hit that poorly with RISP often enough that it isn't super rare, but 3-38 still seems awfully hard to do, and to have won all those games anyway is indeed impressive.
After already beating plenty of good teams this year, there is no reason to over interpret two 1-run losses on the road. Each teams batted ball luck could have easily fallen differently and split those 2 games.
I think part of the difficulty with Vaughn in this case is that his splits this season against lefties are just so ridiculous that it throws off our intuitions about the down side of the platoon. .467/.569/.810 makes MVP Bonds look second best.