Surface capture normalization is based on the concept of overloading to normalize. For this to work, the beads capture X molecules. If you add >X, then you get normalized samples as the excess molecules are discarded in washing. If you add <X, then you get not so normalized samples as the beads capture "all" available molecules.
My guess is you are below X as you normalized to 1 ng prior to input. You are also gambling on the lot-to-lot reproducibility of the kit at that low of a range. What does the manufacturer recommend as input range?
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