There's really not any good AK2i skin editors.
The official(?) one doesn't work, as you've seen.
And the one from
Dan Taylor has numerous problems with things like alignment (what you see is not what you get), compression (it doesn't use the best compression so you end up with low quality images) and conversion (it will convert images that are already BMP15 over and over giving you a very distorted image).
I would suggest looking at what images are in another theme, borrowing the INI files as a base and pretty much doing it all in an image editing program.
I should also note that skins I've made don't have the same colors on the DS (I think they end up darker) -- this could just be my set up, or it could be my settings or it could be the way AceKard/AKAIO/Wood renders. I haven't really played around with it much, but I did not have this problem with Moonshell2 (uses PNGs) or R4/YSMenu ('normal' BMPs) skins.