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I almost exclusively start between 1090 and 1094, and even when the ERE is small in comparison to the Turks, they still always win.
The Muslims in Andalucia always lose too.
I'm not sure, but it might be because Muslims don't join each other's Jihads? At least they didn't the last time I played, which was a couple of versions ago. Compare this to the Catholics, who always have close to 100% moral authority, and win every crusade which the player isn't involved in due to the massive number of participants. I hope this will be resolved at some point, but I don't really know how to resolve the issue.

Funny. I usually see the Muslims win in Iberia in 1000/1066. I practically only start in 1000, though.
 
The Seljuk conquest of Anatolia had less to do with the defeat at Manzikert than it did with the decade of civil war between Romanos Diogenes blinding and Alexios Komnenos's accession in 1081. Many historians have shown that the conquest of anatolia was gradual and mightily assisted by the internal conflict.
The circumstances would need to be similar in my opinion for the Seljuks to win every time.