As for why the windows broke, the building was hermetically sealed. Add one jumbo jet of plane then the pressure rises and about one jumbo jet of air will want to exit. (Less because air is compressible. Once air pressure can equalize, then more because the internal air pressure is above the outside air pressure. The need to maintain different air pressures is one of the reasons for not allowing open windows.) Do this while you have just put the structure through unusual stresses and strains (eg from the transmitted shock), and you will manage to remove a lot of windows.
Additionally do not discount the effect of the ball of fire. Rapidly heating structures with components made of different substances can cause serious damage from differentials in their expansion rates.
Cheers,
Ben