Yes, I also did the same with the mid, and erased all crowns in the 3( headgear, mid, behind) before copy and pasting the desired helms.
Code:name = "PORTRAIT_darknutgfx_male" effectFile = "gfx/FX/portrait.lua" layer = { # GFX_TYPE:[d|p]INDEX:COLOR_LINK:DONT_REFRESH_IF_VALID:CULTURE_INDEX "GFX_character_background:p0" "GFX_western_male_clothes_behind:p3:c0" "GFX_darknut_male_headgear_behind:p5:c1" "GFX_western_male_hair_behind:p1:h:y" "GFX_western_male_beard_behind:p4:h:y" "GFX_western_male_base:p2" "GFX_western_male_neck:d0" "GFX_western_male_cheeks:d4" "GFX_western_male_chin:d1" "GFX_western_male_mouth:d2:o75x49" "GFX_western_male_nose:d3:o80x65" "GFX_western_male_eyes:d6:o47x74" "GFX_western_male_eyes2:d6:e:o74x92" "GFX_character_scars:p7:y" "GFX_character_reddots:p8" "GFX_character_boils:p9" "GFX_character_blinded_eyes:p10" "GFX_western_male_clothes:p3:c2" "GFX_darknut_male_headgear_mid:p5:c3" "GFX_western_male_ear:d7:o27x54" "GFX_western_male_beard:p4:h:y" "GFX_western_male_hair:p1:h:y" "GFX_western_male_clothes_infront:p3:c4" "GFX_darknut_male_headgear:p5:c5" "GFX_character_imprisoned:p6" "GFX_player_overlay:p11" }
Did you correct the alpha layers on the relevant files? It sounds like the old alpha layers is still being recognized.