From my experience of playing DSLR
the skipping in dim environment is probably because of insufficient CPU performance. When the light is dim, slower shutter speed and higher iso is required to obtain proper exposure, thus increase the noise. More cpu resource is needed to perform noise reduction. Then if the cpu is not strong enough, it skipps

If you take photos you know when you use high ISO and noise reduction at the same time, speed and the maximum frames of continuous shooting is usually affected.
So from my view, if we cannot improve the algorithm of encoder to achieve higher efficiency(which I think is quite difficult), then force disabling the noise reduction might be a way to solve this, although the video will be noisy...
just guessing...
