After numerous phone calls to the NJ Tax Practitioner Hotline to explain the problem, they finally gave me the following answer after presumably checking with the department who made the change - "If the amounts from the lower tiered partnership include state modifications, then the difference between the state and federal amounts will be entered into line 13b (if the state amount is a positive difference) or line 15e (if the state amount is a negative difference), respectively."

This does fix the problem, but it would have been nice if the instructions to Form 1065 indicated this.  LaCerte is not handling the adjustment automatically (probably because the adjustment is not addressed in the instructions) so it is necessary to make a manual adjustment. 

Hope this helps.