Assembling JST PH connectors
Did you use the correct pin crimp tool, either YRS-240 or YRM-240?

http://media.digikey.com/pdf/Data%20Sheets/JST%20PDFs/Hand%20and%20Crimping%20Tools.pdf

These tools run around $1000 each, and are kinda tricky to use. If used correctly though, these make perfect crimps.