I still don't agree with the whole "negate doesn't negate" thing. Being immune to criticals doesn't negate the critical effects, that I can easily and readily agree with, but the fortification is designed to make the critical go away as if it never happened.
Flaming Burst isn't an effect onto the target creature, it has only to do with the weapon itself. When the weapon criticals, it suddenly explodes with fire and deals extra flame damage because of that. Of course, the hit from the weapon itself wouldn't deal extra damage, but the flame damage is still larger because the weapon is a fiery weapon of flamey-death.
A vorpal weapon would have to get through the fortification to actually be able to have the head popping effect. Meaning that, upon successful negation of the critical hit (depending on the type of fortification) you negate the vorpal effect as well.
At least,that's how I'm seeing it.