After confirmation from ST (TECH040370), I replaced STM32F407VGT6 with STM32F427VIT6 controller on my device. I did not change driver layer in firmware since its pin to pin compatible replacement. After replacement I could download the code into controller using JTAG and make it run. I see LEDs flash as per expected. The only thing not completely working is Ethernet communication. The device is not responding to any Ethernet request sent to it. The device is able to transmit packets over network but not receiving anything. That means I see ARP requests being sent by device on power up and later. The only problem seem to be with receive. I tried EMAC loopback mode and I found that all packets transmitted is received correctly. So I am not able to understand where the problem is. I also referred Migration from "Migrating from STM32F407xx/417xx to STM32F427xx/429xx/437xx/439xx" document given by ST. This does not mentions anything EMAC related. I verified all EMAC registers holds same values as previous. I verified this on two different boards and results are same. That means soldering is not problem.
Please give me the pointers. Your help is appreciated. Thanks!