NHervé: On which homebrews? I've tested compared a few homebrews on Desmume with the real thing, and they were perfect. And, also, I've tested a few hundred ones and compared with author done screenshots and looked OK. Of course, I could have missed something :P
About AVI capturing, keep in mind that desmume uses BGR 15 bit color for the emulated screen buffers, I know it's rare, but that's how official version works :P