Any ammo detonation leads to a cook off which guarantees death of the crew. This is not modeled correctly there is no data which would lead to believe that a modern retrofitted vehicle with exterior ammo would suffer adverse effects from burning ammo on the outside of the tank.
I have also been having the same issues, even when I try to use FPE the stupid thing keeps burning for no reason and never has enough time to try and use the 2nd one as the outside missile tubes are burning too quickly and with the heat of 1,000 suns for some reason cause the rest of the interior to turn into a oven within micro-seconds and even set off the fuel tank. Seems to be a issue since before this post and is highly annoying. I would rather to just get ammo racked and die all together instead of bursting into flames and burning down faster then a tumble weed through a forest fire.