Depending on the chemistry of your scale inhibitor and it's use rate, these products can and do exibit surface active properties that may have the ability to emulsify some additional oil into the produced water. The trade-off is scale inhibition versus a higher produced water oil content, which is a decision you have to make.
I'm inclined to think that the increased presence of iron sulfide is not related to your use of a scale inhibitor, but rather a factor related to the producing formation and/or the presence therein of sulfate reducing bacteria, controllable with an appropriate downhole biocide.