"indicate that this is not a portfolio sale"  The point of this is mainly to not subject it to Net Investment Income Tax. Is that a potential issue in this return? Might there be input to say not subject to NIIT?

Or is there an adjustment field for Form 8960 Line 5b? or maybe 5c. 

Or is there investment interest expense? 

EDIT: P.S. I don't use ProSeries but maybe these hints help you find what you're looking for.