My project is based around the ATMEGA32u4 microcontroller.

I followed the Arduino Pro Micro schematic to design my own board layout and build a custom PCB, soldered on the components. Then I used the Arduino IDE to successfully upload the Arduino bootloader with SPI.

Currently I can also upload programs to my `32u4 over SPI (using "in-serial programming"). Tested that with Blink.

But I cannot upload programs with the USB, like you would normally be able to do with a Pro Micro. What things should I look for to debug this?

avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53
     Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
     Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "C:\Users\Myname\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino9/etc/avrdude.conf"

     Using Port                    : COM12
     Using Programmer              : avr109
     Overriding Baud Rate          : 57600
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : butterfly
     Description     : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding