This occurs with any of the modes using the top screen, but setting it to use the bottom screen works perfectly fine (see attached photo). It also occurs with both 0.9.1 and 0.9.0 (I haven't tried any of the older 0.8.x versions) and also occurs regardless of whether the cia or the 3dsx variant is used.
Even when using a configuration file taken directly from a working original 3DS system (which does not have this issue), I still end up with this problem. Both systems were similarly softmodded in exactly the same manner save for the initial exploit used (soundhax on the 3DS; safecerthax on 2DS).
Despite the attached photo being taken while the mgba menu is up, it still displays the game on the top screen in the very same manner even when actually playing the game and not in the mgba menu.
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You're right, it works perfectly fine in 0.8.4 though performance is quite a bit worse than 0.9.0, sometimes as much as 10 frames or so (btw is 0.9.0 supposed to perform better than 0.9.1? Because it does, not by much, but maybe 3 to 5 frames).
I tested 0.8.4 and the performance in Pokemon Pinball is a vast difference between versions. 0.8.4 does display 90FPS or so when the game feels much slower. Not sure if 0.9.1 is again faster or slower than 0.9.0. I tested the build that was posted above and that seems to fix the issue.