I am getting the same diagnostic; the 1040X is placing a negative number into Taxable Income instead of the zero per instructions.  

I paged through 29 of 44 pages of Lacerte Diagnostics to find this very unhelpful insight into ref #54276.  

Overriding with a zero in screen 59 does nothing to fix this.  This is a calculation error in Lacerte it appears.  

Since the error refers to "e-file:  Form 1040-X:  the Original amount and Correct amount for the following items cannot be negative for e-file purposes: QBI, Taxable Income and EIC ref 54276", and the 1040X is showing a negative Taxable Income instead of a zero per IRS instructions on the 1040X itself, with QBI and EIC as positive amounts, I am thinking that this is the problem, as it is the only negative number in the Original amount or Correct amount columns of any of these scenarios.  There appears to be no fix for this.  Please advise.