Scrubbing alone/BKF, will not remove rust completely, which is why we use a Vinegar bath or electrolysis AFTER the lye bath. (The BKF will help neutralize the lye).
In many instances, black spots may indicate buried, deeper pockets of red rust.
It is difficult to asses rust by visual inspection alone.
I would re-strip in the lye bath, and then do a de-rusting treatment with the objective of completely removing the remaining dark areas. :)