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Oh, right. On Android and Windows input is read asynchronously on a separate thread. On SDL, it's only read on video flip, which might be the issue there. Not sure if SDL even allows reading input on a separate thread.
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Ok, still stuttering a lot with a better power supply, but I don't think it's PPSSPP's fault.
sysstat is showing huge wait% spikes when this happens. I suspect my no-name brand SD card isn't performing consistently.
Will update again once I switch cards.
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Confirming that the latest GIT build fixes stuttering and Maverick Hunter X hang.