Is this your only CA return? 

Section B, 3 Business Income or (Loss) - The first column is just repeating the same information that is on the 1040. Columns B & C are for adjustments due to changes in CA law. 

It has absolutely nothing to do with W-2 or (for ProConnect 1099) 

" (The income was actually a schedule C loss of about $4.6K)" means line 3 should have (4,600) on it.