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EDIT, some hours after...
Well, no one has responded here I use my own wrong double post...
... I was thinking ( i can wrong again, dont worry )... Not be a solution re-make the skin problem?, =)...
I'm not saying do it all again with details and everything ... I say only: open the skin with DXT1, move it to editor (in my case, I use Paint.NET program, being simple and effective), maybe make some "very small" modification, re-save as a bitmap, draw the alpha channel, to add new skin ... finally save the file as a DDS DXT5 (512x512) y. .. finally save it in the folder "textures".
Then, i was feeling to free work in it... i make a new skin (as if I were making a new skin, but not), i make some graphic modications (only for test, this should not be the version to be used in the game)... i test it in some custom battles, and seems work fine.
In short, pardon me if I havent good explained, the general idea is to make new files on skin problems, while retaining their original appearance (it's the idea, if we can take to make changes too).
hummm... well, if you want test, test it:
... if im wrong again, sorry, i only want help.