Clay, I always do Lye Bath before Electro.. keeps the electro running 'mean and clean'. :)
That said, what I have found is those annoying black spots usually are harboring bad rust underneath.
During scrub down with cold water after electro, I keep a spray bottle of white vinegar handy and give a little squirt on the 'black spot', let sit for about 2 minutes, then scrub with SS scrubby under running cold water. Watch the color of the rinse water. Usually a reddish hue will show.
Back to the electro, and then scrub again.
The downside is,,, usually that black spot will eventually reveal a bit o pitting.... :'( :'( Now you have successfully pried a 'secret' outta me! ;D