Homemade Arduino Leonardo not working

I had a couple of ATMEGA32U4s lying around from an earlier project and I thought why not make a Leonardo for the odd prototyping purposes. In the process I thought it might make sense to make the board compatible with Atmel Studio C code as well and hence you see ports named as per the 32U4’s datasheet as well. The schematic is attached here (its not really a Micro, just the name is erroneous and I never bothered to correct it).

Now after building the board, first I used the Pocket AVR Programmer to flash the 32U4 with the Arduino bootloader (by reading through Sparkfun’s excellent hookup guide). This went off without a glitch and I did not get any errors. However, after this when I connect the standalone board, The TX and RX pins are on all the time and I don’t think new HID+COM ports are being created for the device since the Tools > Ports is greyed out. What am I missing here?

Arduino Micro revA.pdf (83.7 KB)

Are fuses set correctly?

What's the layout look like?

I don't like the look of that crystal select jumper thing, though I don't have a good feel for how sensitive the crystal lines are to layout.

I don't think I've ever seen clocks setup like that, the usb on computers are fussy, those pins are acting like antennas to one another and could definitely disrupt the frequency. You're not even supposed to put a ground plane under crystals ( not that you did, its just that's how sensitive they are)

tom10122:
You're not even supposed to put a ground plane under crystals ( not that you did, its just that's how sensitive they are)

Wow didnt know about that, do you have a reference? This may explain some troubles Ive had with crystals.

Thanks folks. The crystal setup is essentially a selector between 16M and 8M depending on what the user wants to choose. The fuse bits seem ok. They read:

lfuse: 0xff
hfuse: 0xd8
efuse: 0xcb

I did not know about not laying a ground plane below a crystal. Right now there are jumpers to select the crystal. If I were to remove these jumpers and solder the pads would that help?