If you have a horse from another mod that that uses MP_Horse_01_Hand_000 or P_C_Horse_01_Hand_001 then that horse will always show up female. 

In order to fix this, you can either change that horse's model to P_C_Horse_01_Hand_000 or delete MP_Horse_01_Hand_000.ydd, P_C_Horse_01_Hand_001.ydd, and SheathAlbedos.ytd from this folder.