USB IO Board Arduino Micro Clone PID/VID changed

I've researched several of topics on this forum relevant to my problem but I have yet to find a solution. I've created an arduino clone based off the arduino mico platform integrating the atMega32U4. I've recompiled a new bootloader, using the makefile currently in the Arduino --> Hardware --> arduino --> bootloaders --> caterina folder. The problem exists as the following:

  1. Flash the bootloader, fuse bit, and lock bits using an Arduino ISP.
  2. Connect my arduino clone to the computer and it identifies as the correct board name with the right PID/VID values.
  3. Next, I added my custom board to the boards.txt file with its respective attributes (PID/VID, fuse bits, lock bits, etc.)
  4. Open Arduino IDE, select my board, and I'm able to upload any working sketch to the board.
  5. However, after it is flashed, the board is identified as a USB IO Board with the PID/VID values intact.

Has anyone come across this issue? How have you fixed it? I've tried so many possible solutions but none of them work. I've even tried this across multiple arduino clones, same issue.

I'm happy to provide more details should someone request them, but at this point I will really appreciate if someone can point me to the right direction. I'm on a MAC and I've tried plugging this into windows machines but I run into the same problem.

Thanks again for your help.

These are some of the resources I've used.

http://www.ladyada.net/learn/avr/avrdude.html
http://forum.freetronics.com/viewtopic.php?t=663
http://forum.arduino.cc/index.php?topic=57795.0