It's for cross-checking the data that ends up in the FMGECs against each other. It's not for checking the entered data against max/min values or anything else along those lines - it is an internal comparison only.
The data in both FMGECs is synchronized. They don't compute the CG/ZWF initial data. It's a pure mechanical entry and there is no reason for them to be different like any other pilot input. Yet the message comes quite often.