Hi Akshay:
I think you need to change the driver, please take special attention to the module
init_enet.c (C:\Freescale\Freescale_MQX_4_2\mqx\source\bsp\[twrk60n512])
phy_ksz8041.h and phy_ksz8041.c here is where the phy is initialized.
The changes should apply according to the specifications of your Phy.
After you perform all the necessary changes in the BSP, it is necessary to recompile the libraries.
Hope this information is helpful, Have a nice day!
Regards
Daniel