Are you sure that you are using MQX in your project??
I had this problem, too. Response from the support:
The MQX V4.0 has been released 1 week before the MCU V10.3.
The MQX V4.0 installer doesn’t recognized (found) the MCU V10.3 installation.
To avoid problem, you must install them.
Launch MCU V10.3 and install patches Help | Install New Software …
Select FSL MCU Eclipse Update Site - http://freescale.com/lgfiles/updates/Eclipse/MCU10_3/com.freescale.mcu.updatesite
Click on Select All, please sellect all, this is important.