Hey Aaron, that's an odd one that I've never seen before. I know you will have tried this, but I'll suggest it anyway:
Exit controller
Unplug machine usb
Unplug machine power
Restart PC
Plug in machine usb
restart controller

Assume you've done that.
Open the arduino IDE and start the serial monitor with 57600 baud rate. See if anything is coming from the machine. IF it is something "normal looking" (ie not a stream of gibberish), then try sending it some commands (any random characters will do) in the serial monitor and check that doesn't throw it into panic mode. It won't do anything, and should reply with a sane "cannot be parsed" message.

It looks like the machine has been sent some odd non-ascii codes, that sometimes happens when the baud rate is wrong, but if you haven't changes the code that won't be it. Now the 5x repetition of "Comm (MSG,E," could indicate some kind of looping problem, but it's just as likely to be a simple output of the 5 parameters that are allowed in a standard polargraph command. Maybe the memory has been corrupted somehow.

The motors really are very separate from the actual logic, and in fact the motors don't even need to be attached to run the code, so no comms behaviour could ever be affected by bad motors.

Can you re-upload the firmware? Might just straighten this snag out.

sn

Aaron, Sandy is suggesting re-uploading the pre-compiled firmware .hex file to your arduino, or opening the source .ino in the IDE and compiling/uploading from there (your choice of methods, both have the same result).

You're using polargraph_server_a1 on an uno with an adafruit motor shield?

Well, this is weird.

I uploaded the .ino file, after tweaking it for use with the Adafruit motorshield v2 and I'm still getting the same problem!

That was a puzzler. I wonder if there was a short, and that was causing odd characters to be generated, which were interpreted as inputs to itself, and caused the machine to fire off an error message. Who knows! Glad its fixed.

sn