If the ecm is unable to control timing you will see disparity. Code 42 indicates that the ecm is unable to put the module in "EST" mode where it will accept timing signals from the ecm. A faulty ecm is one possible cause of code 42.

You could confirm the engine is running on module timing by watching for relatively fixed timing at the balancer from idle to 1600-2000 rpm with a rapid increase in advance above that.