I've been able to get to the bottom of my issue and wanted to share what I tried in case it helps others. I used the software serial library to receive the input from the midi circuit and mirror it back to my computer using the usual serial methods. Doing this I discovered that my midi device was sending a 11111110 byte down the wire near constantly. This is a "Active Sensing" message, it's a normal thing for a midi device to do, but just something I was unaware of. So what I though was a short, was actually my arduino board dutifully receiving midi and notifying me about it!