@Franklhats did you ever get this problem resolved?  We are having the same issue.  I finally unchecked the DD boxes on the offending checks, but also now have that negative balance in our payroll account in QB showing up.  I will be working with my bookkeeper this week to see what we can do to "fix" the problem so the balance is back to ZERO, but I am afraid that we might have duplicates of payroll / deductions / taxes, etc.