I think I know where the issue is.
The obedience modifier is not an integer anymore, but a float number. Enchanted items can increase it by 0.05-0.15 (if accessories) or 0.15-0.30 (if clothes). In enchantments.gd there's a line that rounds their effect: being the modifier always less than 0.5, the function returns zero. Suggested fix: replacing
enchant.effectvalue = round(rand_range(tempenchant.mineffect, tempenchant.maxeffect))
with
enchant.effectvalue = round(rand_range(tempenchant.mineffect * 100, tempenchant.maxeffect * 100)) / 100