Custom motion controller board, making weird PWM noises?

Hi guys,

I've created a custom motion controller for my new RepRap based pick and place / 3D printer:
[hackaday.io]
[github.com]
COMPLETELY open source, btw.... let's get that out of the way.

I'm finally getting it running, and it seems like when the motors are enabled, I'm hearing this weird repeating pattern of pwm noises. I'm watching the stepper signals on a scope, they'll do the PWM and then just go to the +12V rail for a sec and then back to PWMing. Here's a cellphone video that demonstrates the problem:

[www.youtube.com]

And here's some references for my design. It was inspired from RAMPS and Melzi, and uses the StepStick controllers, and a 20 MHz Atmega1284P. Emphasis was on completely SMT design (well almost), with a modular tool system that doesn't really matter for the context of this thread :-)

Github Repo: [github.com]
Schematic: [github.com]
It runs modified Marlin: [github.com]
And needed a custom Arduino hardware definition because sanguinololu didn't support ATmega1284p at 20 MHz: [github.com]

Anyway, I was wondering if any of the old-timers around here have ever heard anything like this, and if there's anything that I should check. I'll keep looking at it, but figured this was a great resource to bounce ideas off of.

Thanks!

-Neil