I play a Heretek with the machine trait.

Do all armour points apply against fire damage or only the armour points gained from the Machine (x)?

Tunafishsalad said:

Only your Machine (X) trait. The damage from being set on fire ignores armor by default, but the machine trait specifies that its armor bonus applies anyway. Keep in mind that shots from a flame weapon still allow normal armor bonuses to be applied against the weapon damage, it's only the 'set on fire' effect that hoses your non-machine armor.