I totally have same problem mentioned in this link "Using FlexCAN with KSDK and MQX RTOS ".
Since just one Message Buffer can be set to a one CAN Device, I am able to receive only one messageID. I used the PEx CAN_LDD component, it was working fine. But in my new project I have to use ksdk 1.3 CAN Device but I do not know how to solve this problem. Does anybody have any idea?