Here is the gamesetup i run:
Custom Game : Standard empire
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1400 Stars
15 x 15 sectors
Expansion : PreWarp
Aggression: Chaos
Difficulty: Extreme
Research: Very Expensive 480k
Creatures: Many
Pirates: Very Many -> Prox: Average
Pirate Strength: Strong -> Destroyed pirates do no respawn
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Colony Prevalence: Occasional
Independent Life: Rare
Colony Influence Range: 125%
Enforced Colonization Range Limits: 2.00 sectors
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Human
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Home System: Normal
Size: Starting
Tech Level: PreWarp
Corruption: Low
Government: Democracy
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Auto-Generate Starting Empires: 24
Disallow independant alien colonies to start new empires during the game
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Territory: 95%
Population: 95%
Economy: 95%
Dissallow race specific victory conditions
Victory Conditions apply after 25 years
Enable Original Distant Worlds Story Events
Enable Return of the Shakturi Story events and conditions
Enable Disasters and other events
Enable Race Specific Events
Enable Shadows story events
Allow Tech Trading
Allow Giant Kaltors at Game Start
So after all that, i go into Game Editor to see what races are in the map and there is never Ancient Guardians.
Is the game only randomly putting them in even with the Story Line Enabled?
I have tried reducing the Races down to 20 and down to 15 but that doesnt help.
I have tried mucking about with PreWard start and Tech Levels but that hasnt achieved anything either

Please people help! i love fighting the Shakturi and this is driving me nuts.