Due to a problem in Quartus® II software version 13.1 and earlier, you may see that the phase increment value does not recalculate in the NCO Megacore® GUI whenever you enter a different clock frequency or a desired output frequency.
The problem only occurs when you edit the frequency text fields and then move directly to another field.
To work around this problem edit the frequency text fields then press enter first before moving on to another field.
This problem is scheduled to be fixed in a future release of the Quartus II software.