If you're showing us raws Genex, don't save them as jpeg. That just simply screw up the natural color of the raw with the lossy compression, use png as that's the only format we accept at the moment for lossless. You could run it through an optimizer to reduce the size if you wanted.

Also I hope you're not using denoising from the scanning software, those are not worth if you want a clean result as you can't control locale, otherwise you get spotty noise removal such as your madoka image. It's overfiltered at some areas, and more scanning noise should be removed. I'll just assumed you got those large jpeg artifacts noise from the from a lack of denoising and jpeg compression.

Also this isn't a denoising help thread so i'll end it here.

ps: You can set your scanning depth high but it's unnecessary to upload them at such high depth. Don't really need more than 300-450, if even that high.