I found for the female backsprite that the pallet reverts to default no matter how you edit it. As a test to see what could be edited and I did this:
How it appears in PokeMMO ___ How it looks in NSE
I've tried doing each colour individually but had the same results but when I load it in No$gba it appears as a red silhouette so I know the edit is taking to the rom.
For the record I did give up and managed to make it look alright with the default pallet. I just found it damned annoying and figured I'd mention it with the talk of editing the female backsprite.