The MSR manual says,
"1. Wait for preheat flame to reduce in size (approximately 2 minutes).
If flame goes out, wait 5 minutes for stove to cool before relighting.
2. Open Pump Control Valve 1/2 turn and wait for steady blue flame.
3. Slowly open Pump Control Valve."
So you've been doing it the way they suggest. If you wait for the preheat flame to go out, there's a chance it will cool off too much before you get it lit.
Always remember that you are absolutely unique, just like everybody else. -Margaret Mead