Your VI is busy doing something else (for "at least one or two seconds") until it gets around to acting on the Start button. Do you have some loops with long delays? Do you have VIs before the Start action that take a long time to run?
If you want the Start action to happen before other functions in your program, you may need to restructure your program.
When you say "you have to pull the start button at least one or two seconds" do you mean you have to press and hold the button? In that case, you might consider changing the mechanical action of the switch.
If you can post your VI and give a more detailed description of what you're trying to do, it may show the details needed to solve your problem.
