I think that software is referring to the federal return Sch B, line 9.

On some modules ProSeries will not let us file the Franchise Tax (without turning off error ck, sometimes not at all) if there is anything wrong with federal.

The other solution for Franchise Tax issues is once you have a return you are satisfied with and software is not - enter the answers directly on State Comptroller' website (webfile the form) 

[I am waiting on 2 clients for the webfile code to be able to file either thru ProSeries or directly. Ball is in their court at this point]