Hi Gary,
The most likely it's something with paths either in the .reg file or in the .xml file. The New Project Wizard for MQX shows only the boards that are available in your MQX installation.
To figure out what is installed, first it checks in the .xml file what is the key for this board in the registry - there is a following entry in the .xml file (somewhere at the end of it):
<variable name="MqxInstallRegPath" value="\FreeScale\FreeScale MQX\4.0 CUSTOMK60F120M" conditionId="mcu.mqxprojectwizard1.board.ID_BOARD_CUSTOMK60F120M"/>
Where "\FreeScale\FreeScale MQX\4.0 CUSTOMK60F120M" is the key in the registry. Now you can open the regedit tool and check if the key is there, the full key is:
HKEY_LOCAL_MACHINE\SOFTWARE\Freescale\Freescale MQX\4.0 CUSTOMK60F120M
(The task of the .reg file is to add this key to the registry).
There should be a string value called PATH under this key, with the path to your MQX installation. If this path doesn't exist, the New Project Wizard will not show the board that refers to it.
So this is the first thing to check - if the paths are OK.
The other issue might be that the NPW hasn't been updated to version 1.4.0.
If this does not help, please provide the generated customK60F120M.reg and customK60F120M.xml files, I will look into them.
Best Regards,
Marcin