User-selected frameskip causes slowdowns if the game runs slower than the resulting frame rate, but synchronises correctly if the game runs faster.
Automatic frame skipping is still the default. It now only skips up to 8 frames, but in some games still skips that entire 8 frames. What's needed is an algorithm that averages frame latencies over a few seconds and skips while the latency is LOWER than the average.
This was the entire reason I created the fork, and I finally did it! It syncs the controls every scanline of a frame, which costs about 60,000 MIPS instructions per frame to deal with. Luckily, the processor runs at 396 MHz, which means the cost of checking the controls is 1% of the CPU's power.