Unable to upload code to custom board having ATMEGA2560

Hi all,

A month back 2 of my friends and I started building a new project with a custom arduino board based on Arduino Mega 2560 board. We made a board with the same circuitry as Arduino Mega 2560 (having Atmega8u2 as the USB controller).
We were able to install the bootloader onto the chip and uploaded a sample code to it. But today its suddenly stopped responding.
We checked the com port of the system (its a PC) and it was showing %2560.name% instead of Atmega 2560. While we tried uploading the code, it was showing a timed out error. What could be the problem?

Thank You,
Sanju