Not sure what else to suggest, as I don't have this issue.
Added a new Faction, called Animal.
Set Animal to 50 for all other factions - Hostile, Commoner, Merchant, Defender.
Edit Hostile, Commoner, Merchant, Defender factions to be 50 to Animal.
Global Effect unchecked.
Click OK.
Build - Build Module.
Full detail is good to review what the Animal faction is to other factions, and what those other factions are toward Animal.
It should be 50/50 (purple bar [how Animal faction relates to other factions] / green bar [how other factions relate to Animal faction]) right across.
Another way to test this is to create an empty 8x8 area. Put one of your chickens that is in your Animal faction in one corner of the map, and another on the opposite side. Kill one of the chickens. What is the result of the remaining chicken? Red for hostile, or blue for neutral?
FP!