It would seem that you need to play this rom on DeSmuME 0.9.6 not the newest version.
Can't see the bottom screen to even capture the pikachu. [When you minimize you get all blocky & whited out]

The 2 games I've been getting messy quality on the emulator is Ghost Tricks & Pokemon Ranger.

For some reason when I load my save state from Ghost Tricks [I'm at the part when you need to posses Ray] the Ghost & Trick button is all white. Even worse is when I click Ghost I all I can see is the cores... [Everything loads correctly on 0.9.6] When I try to load Pokemon Ranger I get something similar. But this time I can see the background just not the characters/pokemon nor the mission text that comes up on the screen.

I'll screencap & post them if needed to understand what I mean...

Edit: Both are pretty much on the same settings, though 0.9.7 seems to hate 0.9.6 cheats.