Hi!
I have made my own pcb with a Atmega32u4 as processor. I used the bootloader from Sparkfun (Fio V3). I have a 3.3V power source, 8 Mhz Crystal and the USB-Port is wired just like on the Sparkfun Schematic.
I have “burned” the bootloader via SPI with an Arduino Uno - worked
I uploaded a few sketches to test the hardware via SPI (Upload using programmer) - worked, but it terrible slow!
What i can’t do is using usb to upload. The Board is found in device mangaer as “Sparkfun Fio v3 (COM 15)”. When power the board up, and then want to upload the skech, the board dissapers from the device manager.
In the IDE it just does:
Sketch uses 20398 bytes (71%) of program storage space. Maximum is 28672 bytes.
Global variables use 497 bytes of dynamic memory.
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
A few times until a timeout occurs. The Board seems now “stuck”, it don’t does anything, it does not run any sketch and hitting reset will NOT do anything (neihter execute the programm nor reappear in the device manager).
I have to power down and power up again to fix this.
I tried to initiate Upload, then push reset down, and unpush just the moment it wants to upload, this does something, it starts something that looks like it trys to upload:
Warning: Board breadboard:avr:atmega328bb doesn't define a 'build.board' preference. Auto-set to: AVR_ATMEGA328BB
Sketch uses 20398 bytes (71%) of program storage space. Maximum is 28672 bytes.
Global variables use 497 bytes of dynamic memory.
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, } => {}
PORTS {COM1, } / {COM1, COM9, } => {COM9, }
Found upload port: COM9
C:\Users\Jonathan\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino8/bin/avrdude -CC:\Users\Jonathan\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino8/etc/avrdude.conf -v -patmega32u4 -cavr109 -PCOM9 -b57600 -D -Uflash:w:C:\Users\Jonathan\AppData\Local\Temp\arduino_build_297980/DOGM_test.ino.hex:i
avrdude: Version 6.3, compiled on Dec 16 2016 at 13:33:19
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "C:\Users\Jonathan\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino8/etc/avrdude.conf"
Using Port : COM9
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
avrdude: butterfly_recv(): programmer is not responding
But then it stops 
Any idea how to fix this?
Regards,
Jonathan