it is very strange that when you read an ELISA will give you negative values since any diffraction of the wavelength it will read as a positive value, even just adding pure water it will positive. after you perform the analysis of the ELISA and you subtract the average of the zeros from all your samples, your actual values could become negatives, meaning that the concentration of you samples is below the concentration of the minimal value detected by the ELISA. in that case your ELISA needs to be more sensitive to be able to detect those lower values.