Also, I you have loaded a SAVED mission, each time you reload it, you will have to reassign the runways. If you don't do this, it will default to start the mission in the hangars.
TIP:
If running medium to long range missions, it is good to load the fuel percentage at a good "fighting" level and add Drop Tanks to the plane. The drop tanks will be used first while traveling to target. Once at the target, drop the tanks and you will be left with the percentage that you originally loaded ("fighting" level).