I've had the same issue with the windows. When loading the Cold-n-Dark save (KNKX) my windows are always open. I click on each one and I can hear the audible close sound but they won't close. . .right away. If I wait about 30-45 seconds they will both close. . .strange behavior.  I have set the aircraft reload per your suggestion in another post to Ctrl + Shift + R and when the B-52 reloads the windows will be closed.