I don't think you want to set your phase 1 to zero; otherwise, your pulse train will not be correct. What I believe you want is to change the output polarity. When I configure my counters, the CTR Mode Config VI gets called, and there's an input on this VI to set the polarity. If you set it to low, then I think it will do what you want (it defaults to high, meaning phase 1 must pass before the output goes high).
Mark