The time it takes for the plasma cutter to pressurize the machine torch and initiate an arc is longer on the first pierce than subsequent pierces, this would be the reason for the discrepancy. There is a way to avoid this by manually turning the plasma cutter on briefly by piercing a hole, do this by clicking on Aux then pressing the Plasma button to turn it on and press again to turn off after it pierces a hole, then you can Start your program using the appropriate delay. If you Start another program shortly after you would not have to manually trigger the plasma cutter, only if it sits for a specified period of time, how long that is is plasma manufacturer specific.
Newer plasma cutters have an Ok To Move signal, for use with height control so that you dont have to cycle the plasma cutter to get it to turn on and off faster.