In my mind, the logical progression goes something like this....
Normal:
You roll a natural 20, then confirm the critical hit. Vorpal cuts off the head...immunity to critical hits does not protect from this.
Fortification (100%):
You roll a natural 20, then confirm the critical hit...Then the fortification kicks in and negates the critical confirmation. No critical confirmation, no vorpal effect.
The other possibility doesn't make sense to me....
You roll a natural 20, then confirm the critical. Then the fortification turns back time and makes the crit not happen, but somehow vorpal can sense that there was a confirmation in an alternate time line so triggers anyways, even though the confirmation roll was negated.
I'm skeptical that the intent of the rules is different than this.