Jay,
One more thing to try. I found a VI in the counter->advanced called Counter Set Attribute. One of the attributes, 13, lets you set the count of the counter before it is triggered. If you set your pulse to 50% duty cycle, positive polarity, and then call this VI and set the count to 100,000 (if you are using the 20MHz internal clock) (100,000 / 20,000,000 cts per sec is 5 milliseconds, or the length of phase 1) then when the counter is triggered, it is possible to skip the first phase 1. You must call this VI BEFORE the Counter Start VI.
I've not tried this before, so I'm grasping. Conceptually it should work, but it'd be easy to try it.
Mark