Can only connect to Teensy when it's not on the protoboard

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I'm trying to use the MIDI library with my Teensy 3.1, but I'm running into some problems. I've wired it up as in the docs (https://www.pjrc.com/teensy/td_libs_MIDI.html) and am using pluggable headers to connect the teensy to the protoboard I'm building the rest of the circuit on.

However, I'm seeing some strange behavior—*when connected to my protoboard, the Arduino software gives "Download error" when I try to upload code, and the board won't boot. (It won't boot when powered off USB *or* when powered via external 3.3V)

I've built a second copy of the protoboard, and the same issue occurs. I can't figure out what's going on.

I thought it might be that having something connected to the RX pin would mess up Serial comms over USB, but breaking that connection (nothing on the RX pin now) doesn't solve it.

Edit: photos of the protoboard https://imgur.com/a/QtCBR
 
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Seems the protoboard applies power to the Teensy on 3.3V? If so when connected to USB that will also provide a second source of power and the bottom side trace VIN<>VUSB trace should be cut. In that case the Teensy will need external power when on USB only. Safer to apply 3.7-5.5V on VIN with the trace cut and have the onboard hardware generate the 3.3V.

Not sure if that relates to the problem - but dual power isn't good. Can you post a picture?
 
Thanks for your reply— the protoboard is *not* supplying power, I'm powering it via USB or (to test) via plugging into the top of the stackable headers I have on the Teensy, which I use to connect with the protoboard.
 
Okay - missed half the *or*. Quick look at the schematic - only pin 0 and 1 go into the MIDI circuit on T_3.1. Does it work with wires to just those two pins? Photos would show what and how else it is configured beyond that.
 
See the pics now - nothing is on Pin 0? Pin 1 is GND? The Purple/Green/Yellow are on 23/22/21? Using the card follow the intended pins and post. Check for shorts?
 
Great call, the teensy works off the protoboard with just the MIDI-related pins connected via breadboard. Must be something shorted in my proto, I'll troubleshoot there!
 
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