ATMEGA32u4 Arduino Bootloader Issues

Hey all, I’ve been struggling with this issue for a few days on and off now. I made a custom PCB (schematic below) for a smaller Arduino Pro Micro and it works - mostly. I have been able to burn the bootloader using both an Arduino Uno and with an AVRISP mkII. When I plug the micro into the computer the first time it is recognized as an “Arduino Micro (COM6)”. Then I try to upload the Arduino example Blink.ino sketch - and that works too. In the process the IDE forces the reset and in device manager I can see the “Arduino Micro bootloader (COM7)” replace the micro on COM6. The LED does begin to blink but in device manager it remains as “Arduino Micro bootloader (COM7)”. When I try to upload another sketch to this port it fails (as I would expect) because it cannot force the reset; presumably because the bootloader is already active. So I unplug it and try again. It shows up as "Arduino Micro (COM6); all looks good but when I try to upload it cannot force the reset, tries to upload to “Arduino Micro (COM6)” and fails (I assume because it is not entering into the bootloader).

If anyone has any ideas I’m all ears. Normally I do not have to fight with Atmel hardware like I have this.

That's a great little dev board. Can't understand why it is not more popular.

Haven't used one in couple years, but I remember best source of info for getting started is the Sparkfun "Pro Micro Hookup Guide".

Sparkfun Pro Micro Hookup Guide