It seems that certain games (Link's Awakening, Xenoblade DE) had their fences reached already when posting framebuffers, so the signal that a frame was ready would go out _before_ the frame was enqueued, and the render loop would fail to dequeue anything and "skip" a frame.
This was resulting in their performance lowering dramatically after some loading transitions, as a frame signal would be consumed and presentation would be one frame behind.
It's possible this might have eventually caused deadlocks in these games or others, if it happened twice.
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