Pull-through sharpeners are just WAY TOO LIMITED, in terms of what they will do. They're built on the assumption that the bevels on all knives are more-or-less equal. Bevels either thicker or thinner than what was designed into it will never respond as well. Too-thick edges will only make contact on the shoulder, and too-thin edges will likely be blunted (at least). With thinner edges in particular, I've never liked how these sharpeners pinch the edge between two wheels, or even worse, between those horrid carbide scrapers. The combination of 'pinch-and-pull' just isn't a good way to sharpen, and a great way to damage an edge. I suspect the 'chatter' that you're finding with some blades is exactly the manifestation of that pinching effect. The edge gets grabbed onto, and the chatter is the sound of the edge being repeatedly & violently extricated from that pinching hold. When this happens with the carbide pull-throughs in particular, those things will literally RIP steel out of the edge, sometimes leaving tears/cracks in whatever steel remains behind. The ceramic wheels won't be quite so violent or damaging, but will still likely leave some ugly/uneven/wavy footprints behind.
I've referenced this before, when the topic of pull-through sharpeners comes up, but here's an informative link to some close-up pics of edges sharpened by various different means & tools, including pull-throughs:
Micro Photos of Identical Knives after Different Sharpening Methods
A couple of the relevant pics linked from that site:
(edge produced by the carbide scraper stage of a pull-through sharpener)
(edge produced by the ceramic follow-up stage, in the pull-through sharpener)