Noticed myself having the same issue with Pokemon Fire Red but noticed that the latest build of GBARunner2 for the 3DS that doesn't have this problem is:
https://github.com/DS-Homebrew/TWiLightMenu/releases/download/v17.1.1/TWiLightMenu-3DS.7z
Any later build will have the ripples for this game for whatever reason. I read somewhere that it was just due to the fault of the coding for these games by Nintendo by I dunno. However, the later builds like the one's they're making nowadays have wayy better audio. Too bad the ripple effect seems to be getting worse after every update or so, for particular games.
But if you're tired of the ripple effect on your game, you can keep your current build of twilight menu but extract the GBARunner2_arm7dldi_3ds.nds from the _nds folder in the .7z link I have for you guys!