well thats because of the palette issue,
certain characters share the same palette
pal # 0 is shared with Edgar, Sabin, Celes, Leo, and imp
pal # 1 is shared with Locke, Merchant, and Imperial soldiers
pal # 2 has Terra
pal # 3 is shared with Strago, Relm, Gau, Gogo, Kefka
pal # 4 is shared with Cyan, Shadow, and Setzer
pal # 5 has Mog and Umaro
since Cyan and Shadow share the same palette if u change 1, the other will suffer the consequences,
(the reason Clyde changed things around is because he has Locke's palette, it also depends which 1 u used some might be distorted or have the colors in the wrong order)
if u want to assign different palettes to a character via hex then take a look @ my tutorial, I hope I helped
"Sometimes ninjas do wrong to each other, and in dat way the force of tha earf' comes around da moon - and at that presence, da dirt, it overshadows the grass, so you're like, I can't cut dis grass, there's no sun comin' through. So in order to enable each other the two fruits have to look each other in da eye and understand we can only be right, as da ripe is wrong, you know what I mean?"
-HNIC