Perhaps the code that is used to determine where the AI decides to found its capitol should be reviewed:
Settling 1E or 1SE provides: River, 1 flood plain, cows, horses, clam.
Settling in position provides: Fresh water, wine, pigs, reagents. Settling 2NW provides: Fresh water, pigs, reagents, horses.
Settling in position provides: River, cows, bananas, reagents. Settling 1NW2W provides: River, 2 flood plains, irrigated rice, cows, cotton.
The Ljosalfar have: Fresh water, cows (that they can't develop), mithril (which won't help early game development).
The Clan have: Horses, life mana, with an option on irrigated corn (they must outculture the Khazad to get it).
The Khazad have: Iron (which won't help early game development), with an option on irrigated corn (they must outculture the Clan to get it) - and 4 jungle tiles in their BFC.
In addition to opting for worse starting resources, by relocating these civs have now clustered their capitols. In the cases of the Clan and the Khazad this has limited their options for (close) expansion, and has also put all of them into immediate border contact with other civs (ie early diplomatic penalties that may escalate into early conflict, plus the risk of losing the ability to work tiles of the capitol if outcultured). They all would have been better off just settling in place than moving to where they did (even the Ljosalfar, who would have destroyed the flood plain by doing so). If they were going to move then they all had a much better option that was closer to their starting position than where they settled.