@cbutters: This won't be particularly helpful, but if you're using Calibre's Send To Device, the thumbnails are generated by Calibre, not Nickel, which may explain some inconsistencies.
I'm not familiar with this bit of KOReader's code, but since you mentioned mangas, I'm going to go out on a limb there and say that there may be a size/memory limitation at play somewhere. That wouldn't be the first time something like that has cropped up when talking about covers & mangas...
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