Because the three prongs looks better stylistically than the two. The two is like...it's barely there. A step away from being just a line. It's pretty lame. I don't think it works better for any of The Flashes, they gave it to Barry in Young Justice and in some other animated appearances.
The 3 looks much better artistically. It breaks the fins up nicely and looks like a lightning bolt, the two pronged one looks like two sickles or something, and like little effort went into creating it - looks cheap, the other is simplistic yet complete in the way it looks. Can't mess with the Carmine Infantino (RIP) logo.
The JL Flash logo is like if they did the Batman symbol like this:
Just doesn't look right. Always feels incomplete to me when I look at it.