I have to say this Freescale forum is really quiet, probably due to the relatively low usage of MQX. Anyway, just to help the new comers like me, here is the answer to the question I posted above.
When you are using TWRK60F120M, it uses RMII interface instead of MII, for whatever reasons. The TWR-SER board, on the other hand, has its default settings set to MII mode.
Hence to change from MII to RMII mode, you need to change the following jumpers setting:
1. J2, the CLK_SEL jumper. Short pin 3-4 instead of 1-2. RMII requires 50 MHz to work.
2. J12, the ETH_CONFIG jumper. Default is left open. You need to insert a jumper across pin 9-10. Please check the PHY KSZ8041NL datasheet on the configuration.
Hope this helps.