Another thing you may be running into is that Dolphin compiles shaders (used to emulate certain video effects) on the fly. So the first time these are encountered, there may be some stuttering. They get cached, so subsequent runs should give better performance.
But, the main issues is the one that you already took care of: fluctuating GPU clocks. Same thing happens on AMD hardware too (forcing highest clocks helps reduce stuttering).
But, the main issues is the one that you already took care of: fluctuating GPU clocks. Same thing happens on AMD hardware too (forcing highest clocks helps reduce stuttering).