This appears to be because the GL backend gets confused about the stride when the resolution changes. GL thinks the stride is equal to the width, whereas the core has no such illusions. It's most likely a regression, since I don't remember that issue always existing, especially when I added disabling in the first place.
With a game boy game running and the Super Game Boy border displayed, if you turn off the super game boy border in the settings then the window displays garbage pixels.
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