This happens to me sometimes too. For my situation, here is what I've noticed (may not be applicable to what you're seeing):
I have a tendency to put my sumi into dinky dips and then leave the caps off (if only I could even out the spill marks on the carpeting so it looks less spill-like and more Jackson Pollack looking). Dust gets into the ink and then sometimes lodges between the tines of the nib, impeding ink flow.
Certain kinds of paper I use has a tendency to micro tear as I'm writing. These little smidges of paper also get wedged in the tines sometimes. The wedge makes the tines off center so the slit in the nib doesn't line up. I usually have to clear the wedge with something really thin (I use another piece of paper or the little cleaning plastic film thingie that came with my pilot parallel pen).
This is kind of heretical and I dread what people will say about it but I've also used very fine steel wool (like 000) and rubbing alcohol to clean off some of my nibs which I couldn't get the ink to flow correctly with. I only used it on the top and underside of the nib, away from the tip, closer to the ink hole/reservoir. This is only after rubbing alcohol, toothpaste, spit and determination didn't seem to remove the protective ink repelling coating from the nib. This was a last ditch resort for me (the fine steel wool can also get stuck in the tines and unless you clean off the nib carefully, the wool bits also fall in the ink - not great for sumi...hmmm... maybe not a bad thing for iron gall ink).