DeSmuME has issues with pretty much all frame buffer capture due to the way the screen in it is rendered. If you check the details for the framebuffer in the emulator you'll see that it is 1536x1536 pixels, and only a small portion at the top left is occupied by the game screen itself.
As for WHY it does this, I do not know, but literally ANYTHING will have issues capturing the DeSmuME framebuffer. The best option currently available for this emulator is inner window capture with Aero on.